Definition and Characterization of a “Trypsinosome” from Specific Peptide Characteristics by Nano-HPLC−MS/MS and in Silico Analysis of Complex Protein Mixtures

2004 ◽  
Vol 3 (6) ◽  
pp. 1138-1148 ◽  
Author(s):  
Thierry Le Bihan ◽  
Mark D. Robinson ◽  
Ian I. Stewart ◽  
Daniel Figeys
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Complex Protein ◽  
Silico Analysis ◽  
Specific Peptide

In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

2019 ◽  
Vol 13 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Vishal Ahuja ◽  
Aashima Sharma ◽  
Ranju Kumari Rathour ◽  
Vaishali Sharma ◽  
Nidhi Rana ◽  
...  
Keyword(s):  
Production Process ◽  
In Silico ◽  
Xylose Reductase ◽  
In Silico Analysis ◽  
Emericella Nidulans ◽  
Higher Temperature ◽  
In Silico Characterization ◽  
Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

In silico analysis of selenoprotein N (Gallus gallus): absence of EF-hand motif and the role of CUGS-helix domain in antioxidant protection

Metallomics ◽  
2021 ◽  
Vol 13 (3) ◽  
Author(s):  
Shi-Yong Zhu ◽  
Li-Li Liu ◽  
Yue-Qiang Huang ◽  
Xiao-Wei Li ◽  
Milton Talukder ◽  
...  
Keyword(s):  
In Silico ◽  
Common Ancestor ◽  
In Silico Analysis ◽  
Antioxidant Protection ◽  
Jnk Pathway ◽  
Downstream Target ◽  
Ef Hand ◽  
Silico Analysis

Abstract Selenoprotein N (SEPN1) is critical to the normal muscular physiology. Mutation of SEPN1 can raise congenital muscular disorder in human. It is also central to maturation and structure of skeletal muscle in chicken. However, human SEPN1 contained an EF-hand motif, which was not found in chicken. And the biochemical and molecular characterization of chicken SEPN1 remains unclear. Hence, protein domains, transcription factors, and interactions of Ca2+ in SEPN1 were analyzed in silico to provide the divergence and homology between chicken and human in this work. The results showed that vertebrates’ SEPN1 evolved from a common ancestor. Human and chicken's SEPN1 shared a conserved CUGS-helix domain with function in antioxidant protection. SEPN1 might be a downstream target of JNK pathway, and it could respond to multiple stresses. Human's SEPN1 might not combine with Ca2+ with a single EF-hand motif in calcium homeostasis, and chicken SEPN1 did not have the EF-hand motif in the prediction, indicating the EF-hand motif malfunctioned in chicken SEPN1.

In silico, Physico-chemical characterization and analysis of Sandalwood proteins

2018 ◽  
Vol 3 (02) ◽  
pp. 150-157
Author(s):  
Asad Amir ◽  
Neelesh Kapoor ◽  
Hirdesh Kumar ◽  
Mohd. Tariq ◽  
Mohd. Asif Siddiqui
Keyword(s):  
Secondary Structure ◽  
In Silico ◽  
Chemical Characterization ◽  
In Silico Analysis ◽  
Chemical Parameters ◽  
Physico Chemical ◽  
In Silico Studies ◽  
The Family ◽  
Silico Analysis

Sandalwood is a commercially and culturally important plant species belonging to the family Santalaceae and the genus Santalum. In Indian sandalwood is renowned for its oil, which is highly rated for its sweet, fragrant, persistent aroma and the fixative property which is highly demanded by the perfume industry. For better production and varieties, requires to understanding the functions of proteins, their analysis and characterization of proteins sequences and their structures, their localizations in cell and their interaction with other functional partner. Due to limited number of in silico studies on sandalwood, in the present study we have performed in silico analysis by characterization of sandalwood proteins. Total 23 proteins were obtained and characterization using UniProtKB, identifying their physico-chemical parameters using ProtParam tool and prediction of their secondary structure elements using GOR of all 23 proteins.

In Silico Analysis and Immunohistochemical Characterization of NaPi2b Protein Expression in Ovarian Carcinoma With Monoclonal Antibody Mx35

2012 ◽  
Vol 20 (2) ◽  
pp. 165-172 ◽  
Author(s):  
Ibere Cauduro Soares ◽  
Kleber Simões ◽  
Jorge Estefano Santana de Souza ◽  
Oswaldo Keith Okamoto ◽  
Alda Wakamatsu ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Protein Expression ◽  
Ovarian Carcinoma ◽  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis

scholarly journals In silico analysis, molecular cloning, expression and characterization of l-asparaginase gene from Lactobacillus reuteri DSM 20016

3 Biotech ◽  
2017 ◽  
Vol 7 (5) ◽  
Author(s):  
Suresh Susan Aishwarya ◽  
Sellamuthu Iyappan ◽  
Kamepali Vijaya Lakshmi ◽  
Kandathil Narayanan Rajnish
Keyword(s):  
Molecular Cloning ◽  
In Silico ◽  
Lactobacillus Reuteri ◽  
In Silico Analysis ◽  
Silico Analysis

scholarly journals A comprehensive molecular characterization of the 8q22.2 region reveals the prognostic relevance of OSR2 mRNA in muscle invasive bladder cancer

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248342
Author(s):  
Daniel Uysal ◽  
Karl-Friedrich Kowalewski ◽  
Maximilian Christian Kriegmair ◽  
Ralph Wirtz ◽  
Zoran V. Popovic ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
In Silico ◽  
Copy Number ◽  
In Silico Analysis ◽  
Copy Number Alterations ◽  
Muscle Invasive Bladder Cancer ◽  
Mrna Gene ◽  
Muscle Invasive ◽  
Silico Analysis

Technological advances in molecular profiling have enabled the comprehensive identification of common regions of gene amplification on chromosomes (amplicons) in muscle invasive bladder cancer (MIBC). One such region is 8q22.2, which is largely unexplored in MIBC and could harbor genes with potential for outcome prediction or targeted therapy. To investigate the prognostic role of 8q22.2 and to compare different amplicon definitions, an in-silico analysis of 357 patients from The Cancer Genome Atlas, who underwent radical cystectomy for MIBC, was performed. Amplicons were generated using the GISTIC2.0 algorithm for copy number alterations (DNA_Amplicon) and z-score normalization for mRNA gene overexpression (RNA_Amplicon). Kaplan-Meier survival analysis, univariable, and multivariable Cox proportional hazard ratios were used to relate amplicons, genes, and clinical parameters to overall (OS) and disease-free survival (DFS). Analyses of the biological functions of 8q22.2 genes and genomic events in MIBC were performed to identify potential targets. Genes with prognostic significance from the in silico analysis were validated using RT-qPCR of MIBC tumor samples (n = 46). High 8q22.2 mRNA expression (RNA-AMP) was associated with lymph node metastases. Furthermore, 8q22.2 DNA and RNA amplified patients were more likely to show a luminal subtype (DNA_Amplicon_core: p = 0.029; RNA_Amplicon_core: p = 0.01). Overexpression of the 8q22.2 gene OSR2 predicted shortened DFS in univariable (HR [CI] 1.97 [1.2; 3.22]; p = 0.01) and multivariable in silico analysis (HR [CI] 1.91 [1.15; 3.16]; p = 0.01) and decreased OS (HR [CI] 6.25 [1.37; 28.38]; p = 0.0177) in RT-qPCR data analysis. Alterations in different levels of the 8q22.2 region are associated with manifestation of different clinical characteristics in MIBC. An in-depth comprehensive molecular characterization of genomic regions involved in cancer should include multiple genetic levels, such as DNA copy number alterations and mRNA gene expression, and could lead to a better molecular understanding. In this study, OSR2 is identified as a potential biomarker for survival prognosis.

Characterization of a Monoclonal Antibody, D73H, that Maps to a Highly Conserved Region on Fibrinogen Bβ Chain

2000 ◽  
Vol 84 (07) ◽  
pp. 43-48 ◽  
Author(s):  
B. J. Rybarczyk ◽  
M. Pereira ◽  
P. J. Simpson-Haidaris
Keyword(s):  
In Silico ◽  
Coiled Coil ◽  
In Silico Analysis ◽  
Antigenic Determinants ◽  
Human Fibrinogen ◽  
Western Blots ◽  
C Terminus ◽  
Probability Prediction ◽  
Silico Analysis

SummaryThe primary structure of fibrinogen is highly conserved across species, yet often times monoclonal antibodies produced against the fibrinogen of one species will not crossreact with the fibrinogen of another. Herein, we describe the production and characterization of murine MAb, D73H, raised against human fibrinogen. D73H crossreacts with a highly conserved epitope on the Bβ chain of fibrinogen from human, rat, bovine, guinea pig, and mouse. Western blotting revealed that D73H reacted with the Bβ chain of plasmin fragment D, localizing its epitope to Bβ134-461. A 7 kDa band was identified by D73H in Western blots of reduced fibrinogen CNBr-fragments. N-terminal sequencing mapped this fragment to Bβ243-253, further localizing the epitope to Bβ243-305. In silico analysis indicated that Bβ243-305 is predominantly hydrophilic, and surface probability prediction indicated three potential antigenic determinants corresponding to Bβ252-258, Bβ262-269, and Bβ279-286. Further in silico analysis of the crystal structure of fibrinogen fragment D-D indicated that Bβ262-269 (FGRKWDPY) is predominantly α-helical and located on the surface of the molecule adjacent to a bend imposed in the β chain at residue 260, which is near the junction between the rigid coiled-coil domain and the globular C-terminus. A synthetic peptide corresponding to Bβ261-272 competitively inhibited the binding of D73H to the Bβ chain of denatured intact fibrinogen and reduced and denatured Bβ chain in Western blots, experimentally proving the validity of these predictive algorithms. Together these data indicate that, although plasmin resistant, Bβ chain residues Bβ261-272 comprising the D73H epitope are highly conserved across species, surface exposed, and immunogenic.

Sign in / Sign up

Export Citation Format

Share Document