Performed Protein-Protein Docking, AMITY University, Jan 2020 - Jun 2020
A Mini Project had been done in Bioinformatics subject on "Structural Dynamics of SARS CoV-2 Spike Protein-Angiotensin-Converting Enzyme 2 Complex as Key Panoply for Medical Countermeasures" under Dr. Amresh Prakash at Amity University. The mini-project lasted for about 6-month and had been done on under Dr. Amresh Prakash and Dr. Ravi Dutta Sharma at Amity Institute of Biotechnology in Amity University Gurugram.
Description:
In this project, we investigated the indels/mutations of the novel SARS-CoV-2 and examined the structural aspects involved in the binding of nCoV’s S-protein to the host’s ACE2 receptor by means of homology modelling, protein-protein docking and MD simulation. The obtained 3D structural analyses results revealed the emergence of “MYRISTYL” site along with an RGD peptide sequence on the surface exposed subunit, S1 of SARS-CoV-2. We proposed that the N-terminal attachment of myristoyl lipid anchors to a glycine residue (in RGD motif) oô€ƒ ered ô€ƒ–exibility to the backbone’s conformation and plausibly re-directs reversible S-protein membrane and protein-protein interactions, hence; building a highly stable nCoV S-ACE2 complex for aggravated host tropism. Thus, the interfacial residues underlying nCoV-ACE2 complex interactions could be explored as potential targets for therapeutic interventions of COVID-19.
Skills developed during project :
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Protein-Ligand Docking with Schrödinger Glide in Maestro environment
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Ligand Preparation and Design with LigPrep & Virtual Screening of various compounds
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Protein Protein Docking via ClusPro and Z Dock
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Performed ÄKTA Start Protein Purification & Characterisation, GE Healthcare, Mar 2019 - Oct 2019
A compulsory training program was conducted by Amity Institute of Biotechnology in a collaboration with GE Healthcare, India. Anion exchange chromatography of Bovine Serum Albumin (BSA) was conducted using ÄKTA Start system.
Description:
The training period consisted of protocols which helped us understand the practical principles of anion exchange chromatography by taking step-by-step through the purification of Bovine Serum Albumin (BSA). ÄKTA start was an easy-to-use chromatography system that automated manual purification procedures using HiTrap columns. A system was prepared where bottles containing both buffers were placed. Manual run was done once the columns were connected and a ô€ƒ•final run performed once sample was loaded. After the ô€ƒ•final run the result was seen in the Evaluation module of UNICORN start. ÄKTA start supports commonly used chromatography techniques like desalting/buffer exchange, affinity, gel filtration, and ion exchange. Using ÄKTA start we could perform typical applications such as purification of affinity tagged proteins, antibodies, untagged or native proteins, and sample clean-up. UNICORN system control software, especially designed for ÄKTA start, included a process picture map for real-time monitoring and the intuitive method editor and evaluation modules.
Skills developed during training:
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UNICORN system control software
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ÄKTA Start and ÄKTA Pure system
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About AKTA Start
ÄKTA start is an easy-to-use chromatography system that automates manual purification procedures using for example HiTrap columns. It offered an entry level chromatography solution for the preparative purification of proteins in lab scale.
The system had various
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Intuitive touchscreen display and real time monitoring
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Compact solution for quick and reliable one-step protein purification
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Quick start methods and templates for common purification techniques
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Sample injection and fraction collection options
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The system was easy to use and had an intuitive design, front-facing work area, visible flow path, and a user friendly interface. ÄKTA™ start makes it easy to purify proteins with predefined quick start and editable method templates, real-time run control and visualisation, and single-click operations, together with a compact and portable size suitable for cold-room operations. The instrument could be controlled either in standalone mode using the instrument touch screen display or using UNICORN start control software on a computer.
ÄKTA start supports commonly used chromatography techniques like desalting/buffer exchange, affinity, gel filtration, and ion exchange. Using ÄKTA start we could perform typical applications such as purification of affinity tagged proteins, antibodies, untagged or native proteins, and sample clean-up.
Frac30, a round fraction collector, was controlled via the ÄKTA start touch screen instrument display or using UNICORN start software on a computer. Frac30 allowed to collect up to 30 fractions and supported four tube sizes, ranging from 1,5 ml to 15 ml. Fractions can be collected in volumes ranging from 0,5 ml to 15 ml. The entire fraction collector rack can be transferred as required.
UNICORN system control software, especially designed for ÄKTA start, included a process picture map for real-time monitoring and the intuitive method editor and evaluation modules.