scholarly journals Structural Modeling and Analysis of Pregnancy-Associated Glycoprotein-1 of Buffalo (Bubalus bubalis)

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Jerome Andonissamy ◽  
S. K. Singh ◽  
S. K. Agarwal
Keyword(s):  
Protein Structure ◽  
Active Sites ◽  
Structural Model ◽  
Protein Structures ◽  
Structural Modeling ◽  
Bubalus Bubalis ◽  
High Energy ◽  
Docking Studies ◽  
Modeling And Analysis ◽  
Structural Conformity

The present study was conducted to design and analyze the structural model of buffalo pregnancy-associated glycoprotein-1 (PAG-1) using bioinformatics. Structural modeling of the deduced buffalo PAG-1 protein was done using PHYRE, CONSURF servers and its structure was subsequently constructed using MODELLER 9.9 and PyMOL softwares Buffalo PAG-1 structural conformity was analyzed using PROSA, WHATIF, and 3D-PSSM servers. Designed buffalo PAG-1 protein structure on BLAST analysis retrieved protein structures belonging to aspartic proteinase family. Moreover in silico analysis revealed buffalo PAG-1 protein retained bilobed structure with pepstatin-binding clefts near the active sites by docking studies with pepstatin A using PatchDock server. Structural studies revealed that the amino and carboxy terminal containing aspartic residues are highly conserved and buried within the protein structure. Structural conformity studies showed that more than 90% of the residues lie inside favored and allowed regions. It was also deduced that buffalo PAG-1 possesses low and high energy zones with a very low threshold for proteolysis ascertaining the stableness of the buffalo PAG-1 protein structure. This study depicts the structural conformity and stability of buffalo PAG-1 protein.

scholarly journals PREMONITION - Preprocessing motifs in protein structures for search acceleration

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 217 ◽  
Author(s):  
Sandeep Chakraborty ◽  
Basuthkar J. Rao ◽  
Bjarni Asgeirsson ◽  
Ravindra Venkatramani ◽  
Abhaya M. Dandekar
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Active Site ◽  
Active Sites ◽  
Protein Structures ◽  
3D Structure ◽  
Search Space ◽  
Computational Method ◽  
Computational Time ◽  
Active Site Residues

The remarkable diversity in biological systems is rooted in the ability of the twenty naturally occurring amino acids to perform multifarious catalytic functions by creating unique structural scaffolds known as the active site. Finding such structrual motifs within the protein structure is a key aspect of many computational methods. The algorithm for obtaining combinations of motifs of a certain length, although polynomial in complexity, runs in non-trivial computer time. Also, the search space expands considerably if stereochemically equivalent residues are allowed to replace an amino acid in the motif. In the present work, we propose a method to precompile all possible motifs comprising of a set (n=4 in this case) of predefined amino acid residues from a protein structure that occur within a specified distance (R) of each other (PREMONITION). PREMONITION rolls a sphere of radius R along the protein fold centered at the C atom of each residue, and all possible motifs are extracted within this sphere. The number of residues that can occur within a sphere centered around a residue is bounded by physical constraints, thus setting an upper limit on the processing times. After such a pre-compilation step, the computational time required for querying a protein structure with multiple motifs is considerably reduced. Previously, we had proposed a computational method to estimate the promiscuity of proteins with known active site residues and 3D structure using a database of known active sites in proteins (CSA) by querying each protein with the active site motif of every other residue. The runtimes for such a comparison is reduced from days to hours using the PREMONITION methodology.

scholarly journals Structural Modeling on the Determinants of Effectiveness of SOPs Containing COVID-19 in Mass Gatherings

2021 ◽  
Vol 12 ◽  
Author(s):  
Abdul Basit ◽  
Miklas Scholz ◽  
Abdul Aziz Khan Niazi ◽  
Tehmina Fiaz Qazi ◽  
Muhammad Zeeshan Shaukat ◽  
...  
Keyword(s):  
Literature Review ◽  
Structural Model ◽  
A Priori ◽  
Real Data ◽  
Structural Modeling ◽  
Interpretive Structural Modeling ◽  
Critical Determinant ◽  
Modeling And Analysis ◽  
Mass Gatherings ◽  
Perceived Benefit

The study is aimed to analyze the determinants of the effectiveness of SOPs in mass gatherings for containing COVID-19. The overall design of the study involves a literature review, data collection by field survey, structural modeling, and analysis. The study is built on the experts' opinion of a focus group (representing people who recently participated in and are responsible for mass gatherings). The study uses the discussion of the literature review to identify the determinants, interpretive structural modeling (ISM) for developing and analyzing a structural model, and Matrice d'Impacts Croises Multiplication Appliquée a un Classement (MICMAC) for corroboration of results of the ISM/classification of determinants. From the literature review, a list of determinants is generated and verified by a panel of experts. The results of the ISM revealed that the determinants “legal environment of the country,” “practicability of SOPs,” “perceived benefit of adapting SOPs,” and “possibilities of avoiding gathering” occupied the top of the model, therefore, they are less critical determinants, whereas “nature of gathering” occupied the bottom of the model, and is thus the most critical determinant. The remaining determinants form the middle of the model, and are therefore moderately severe. The results of MICMAC show that the determinant “perceived benefit of adapting SOPs” is dependent, “nature of gathering” is independent, and all others are linked. The results of MICMAC implicitly substantiate the findings of the ISM. The overall results of the study show that “nature of gathering” is the key determinant. This research does not require a priori theory since it is a theory-building study that uses an inductive approach. It is based on real data and it is useful for local authorities, organizers, participants (attendees/visitors) of mass gatherings, health officials/regulators, researchers, and the community at large. This study has fundamental importance for planning and preparing for such events while ensuring the minimum risk of COVID-19 transmission.

Sequence Specific Dihedral Angle Distribution: Application in Protein Structure Prediction and Evaluation

1970 ◽  
Vol 19 (2) ◽  
pp. 217-226
Author(s):  
S. M. Minhaz Ud-Dean ◽  
Mahdi Muhammad Moosa
Keyword(s):  
Protein Structure ◽  
Dihedral Angle ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Protein Structures ◽  
Angle Distribution ◽  
Ramachandran Plot ◽  
Specific Data ◽  
Specific Distribution ◽  
Structure Evaluation

Protein structure prediction and evaluation is one of the major fields of computational biology. Estimation of dihedral angle can provide information about the acceptability of both theoretically predicted and experimentally determined structures. Here we report on the sequence specific dihedral angle distribution of high resolution protein structures available in PDB and have developed Sasichandran, a tool for sequence specific dihedral angle prediction and structure evaluation. This tool will allow evaluation of a protein structure in pdb format from the sequence specific distribution of Ramachandran angles. Additionally, it will allow retrieval of the most probable Ramachandran angles for a given sequence along with the sequence specific data. Key words: Torsion angle, φ-ψ distribution, sequence specific ramachandran plot, Ramasekharan, protein structure appraisal D.O.I. 10.3329/ptcb.v19i2.5439 Plant Tissue Cult. & Biotech. 19(2): 217-226, 2009 (December)

Structural Modeling of Institute of Entrepreneurship in Russia

2019 ◽  
pp. 34-48
Author(s):  
Svetlana L. Sazanova
Keyword(s):  
Global Economy ◽  
Structural Model ◽  
Institutional Environment ◽  
Small And Medium Enterprises ◽  
Structural Modeling ◽  
Entrepreneurial Activity ◽  
Pattern Modeling ◽  
Medium Enterprises ◽  
The Impact ◽  
The Relationship

Entrepreneurship plays an important role in the modern global economy; the share of products of small and medium enterprises in the gross product and exports not only of the developed but also of developing countries is growing. Innovation processes cover all sectors of the economy, and more and more people are involved in entrepreneurial activity, which contributes to the penetration of entrepreneurial thinking and business values in all areas of the socioeconomic life of society. The Institute of Entrepreneurship plays an increasingly prominent role in the institutional environment of socio-economic systems. This actualizes the problem of studying the relationship of the institution of entrepreneurship with the institutions of law, culture, management. This requires a methodology that allows you to explore the impact on the institute of entrepreneurship not only economic, but also non-economic factors. The methodology of the “old” institutionalism possesses such a tool, it is structural modeling (pattern modeling), which allows to explore the diversity of interrelationships of the institution of entrepreneurship with other components of the institutional and economic environment. The article explored the features of the development of the institution of entrepreneurship in Russia, established the relationship between the institution of entrepreneurship, values, motives and incentives for entrepreneurial activity, built a structural model of the institution of entrepreneurship based on the methodology of the old institutionalism (pattern modeling). The structural model of the institution of entrepreneurship reveals the relationship between the institution of entrepreneurship, the values of entrepreneurial activity, its motives and incentives; as well as the relationship between the institution of entrepreneurship with the institutions of governance, cultural and religious institutions, legal institutions and society.

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

Analysis of Oncogene Protein Structure Using Small World Network Concept

2020 ◽  
Vol 15 (7) ◽  
pp. 732-740
Author(s):  
Neetu Kumari ◽  
Anshul Verma
Keyword(s):  
Amino Acids ◽  
Protein Structure ◽  
Degree Distribution ◽  
Protein Structures ◽  
Small World ◽  
Extreme Condition ◽  
Centrality Measures ◽  
Small World Network ◽  
Network Concept ◽  
Oncogene Protein

Background: The basic building block of a body is protein which is a complex system whose structure plays a key role in activation, catalysis, messaging and disease states. Therefore, careful investigation of protein structure is necessary for the diagnosis of diseases and for the drug designing. Protein structures are described at their different levels of complexity: primary (chain), secondary (helical), tertiary (3D), and quaternary structure. Analyzing complex 3D structure of protein is a difficult task but it can be analyzed as a network of interconnection between its component, where amino acids are considered as nodes and interconnection between them are edges. Objective: Many literature works have proven that the small world network concept provides many new opportunities to investigate network of biological systems. The objective of this paper is analyzing the protein structure using small world concept. Methods: Protein is analyzed using small world network concept, specifically where extreme condition is having a degree distribution which follows power law. For the correct verification of the proposed approach, dataset of the Oncogene protein structure is analyzed using Python programming. Results: Protein structure is plotted as network of amino acids (Residue Interaction Graph (RIG)) using distance matrix of nodes with given threshold, then various centrality measures (i.e., degree distribution, Degree-Betweenness correlation, and Betweenness-Closeness correlation) are calculated for 1323 nodes and graphs are plotted. Conclusion: Ultimately, it is concluded that there exist hubs with higher centrality degree but less in number, and they are expected to be robust toward harmful effects of mutations with new functions.

scholarly journals Efficient Catalytic Conversion of Polysulfides by Biomimetic Design of “Branch-Leaf” Electrode for High-Energy Sodium–Sulfur Batteries

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Wenyan Du ◽  
Kangqi Shen ◽  
Yuruo Qi ◽  
Wei Gao ◽  
Mengli Tao ◽  
...  
Keyword(s):  
Active Sites ◽  
High Performance ◽  
Electrochemical Reaction ◽  
Molecular Layer ◽  
Specific Capacity ◽  
High Energy ◽  
Reduction Reaction ◽  
Biomimetic Design ◽  
Co Nanoparticles ◽  
Sodium Sulfur

AbstractRechargeable room temperature sodium–sulfur (RT Na–S) batteries are seriously limited by low sulfur utilization and sluggish electrochemical reaction activity of polysulfide intermediates. Herein, a 3D “branch-leaf” biomimetic design proposed for high performance Na–S batteries, where the leaves constructed from Co nanoparticles on carbon nanofibers (CNF) are fully to expose the active sites of Co. The CNF network acts as conductive “branches” to ensure adequate electron and electrolyte supply for the Co leaves. As an effective electrocatalytic battery system, the 3D “branch-leaf” conductive network with abundant active sites and voids can effectively trap polysulfides and provide plentiful electron/ions pathways for electrochemical reaction. DFT calculation reveals that the Co nanoparticles can induce the formation of a unique Co–S–Na molecular layer on the Co surface, which can enable a fast reduction reaction of the polysulfides. Therefore, the prepared “branch-leaf” CNF-L@Co/S electrode exhibits a high initial specific capacity of 1201 mAh g−1 at 0.1 C and superior rate performance.

scholarly journals Insights on forming N,O-coordinated Cu single-atom catalysts for electrochemical reduction CO2 to methane

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yanming Cai ◽  
Jiaju Fu ◽  
Yang Zhou ◽  
Yu-Chung Chang ◽  
Qianhao Min ◽  
...  
Keyword(s):  
Energy Barrier ◽  
Active Sites ◽  
Theoretical Calculations ◽  
High Energy ◽  
Single Atom ◽  
Faradaic Efficiency ◽  
High Energy Barrier ◽  
Catalytic Sites ◽  
Electron Reduction ◽  
First Time

AbstractSingle-atom catalysts (SACs) are promising candidates to catalyze electrochemical CO2 reduction (ECR) due to maximized atomic utilization. However, products are usually limited to CO instead of hydrocarbons or oxygenates due to unfavorable high energy barrier for further electron transfer on synthesized single atom catalytic sites. Here we report a novel partial-carbonization strategy to modify the electronic structures of center atoms on SACs for lowering the overall endothermic energy of key intermediates. A carbon-dots-based SAC margined with unique CuN2O2 sites was synthesized for the first time. The introduction of oxygen ligands brings remarkably high Faradaic efficiency (78%) and selectivity (99% of ECR products) for electrochemical converting CO2 to CH4 with current density of 40 mA·cm-2 in aqueous electrolytes, surpassing most reported SACs which stop at two-electron reduction. Theoretical calculations further revealed that the high selectivity and activity on CuN2O2 active sites are due to the proper elevated CH4 and H2 energy barrier and fine-tuned electronic structure of Cu active sites.

scholarly journals Factors Affecting the Lut Desert Tourism in Iran: Developing an Interpretive-Structural Model

2021 ◽  
Vol 13 (13) ◽  
pp. 7245
Author(s):  
Beniamino Murgante ◽  
Mohammad Eskandari Sani ◽  
Sara Pishgahi ◽  
Moslem Zarghamfard ◽  
Fatemeh Kahaki
Keyword(s):  
Sampling Method ◽  
Structural Model ◽  
Tourism Development ◽  
Cost Effective ◽  
Structural Modeling ◽  
Interpretive Structural Modeling ◽  
Factors Affecting ◽  
Purposive Sampling ◽  
Interpretive Structural Model ◽  
Lut Desert

The Lut desert is one of the largest and most attractive deserts in Iran. The value of desert tourism remains unclear for Iran’s economy and has only recently been taken into consideration by the authorities, although its true national and international value remains unclear. This study was aimed at investigating the factors that influence tourism development in the Lut desert. Data collected through the purposive sampling method was analyzed using Interpretive Structural Modeling and the MICMAC Analysis. According to the results, cost-effective travel expenses, security, and safety provided in the desert, together with appropriate media advertising and illustration of the Lut desert (branding) are the leading factors that influence tourism in the Lut desert in Iran. This paper highlighted the importance of desert tourism, especially in this region.

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