PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins

Islam, Rifat Nawaz Ul; C, Roy; Pss, Gupta; Banerjee, Sumanta; Mitra, Debanjan; Bandyopadhyay, Amal Kumar

doi:10.6026/97320630014190

Cited by 2 publications

(3 citation statements)

References 10 publications

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“…Now, we have presented Figure 2 to understand the basis of this. Conceptually, a protein is a thermodynamically compromise state [ 1 , 36 ]. Therefore, it is normal to have favorable and unfavorable forces in it.…”

Section: Resultsmentioning

confidence: 99%

“…Accessibility is extracted with the help of NACCESS to know the location of these residues in core and surface of protein [ 35 ]. ME's secondary structure information (helix or sheet or coil) is calculated by PROPAB's principle [ 36 ]. Other binary data such as residue class, physicochemical properties, ME-residue's distance from positive and negative partners of salt-bridge are also extracted.…”

Section: Methodsmentioning

confidence: 99%

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Salt-Bridges in the Microenvironment of Stable Protein Structures

2020

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Salt-bridges (sb) play an important role in the folding and stability of proteins. This is deduced from the evaluation of net energy in the microenvironments (ME, residues that are 4Å away from positive and negative partners of salt-bridge and interact with them). ME’s act as a determinant of net-energy due to the intrinsic features by the sequence. The stability of extremophilic proteins is due to the presence of favorable residues at the ME without any unfavorable residues. We studied a dataset of four structures from the pdb and a homology model (PDB ID: 1HM5) to gain insights on this issue. Data shows that the presence of isolated charges and polar residues in the core of extremophilic proteins helps in the formation of stable salt-bridges with reduced desolvation. Thus, site-specific mutations with favorable residues at the ME will help develop thermo stable proteins with strong salt bridges.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Salt-Bridges in the Microenvironment of Stable Protein Structures

2020

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“…Core and surface composition of those structures were identi ed by COSURIM [31]. Analyses of the secondary structure were done by PROPAB [32] to nd the amino acid abundance in coil, helix and strand.…”

Section: Analysis Of Crystal Structurementioning

confidence: 99%

Comparative physicochemical and evolutionary study of SARS-CoV-2 and SARS with special reference to salt bridge and their microenvironment: A plausible explanation for divergency, stability and severity of SARS-CoV-2

Mitra

Pal

Mohapatra

2020

Preprint

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The occurrence of concentrated pneumonia cases in Wuhan city, Hubei province of China was first reported on December 30, 2019. Currently, it is known as COVID 19 and now it is a nightmare for the whole world. SARS CoV first reported in 2002, but not spread worldwide. After 18 years, in 2020 it reappears and spread worldwide as SARS-CoV-2 (COVID 19), the most dangerous virus creating disease in the world. Is it possible to create a favorable evolution within this short time? If possible, then what are those properties that are changed in SARS-CoV-2 to make it undefeated? What are the basic differences between SARS-CoV-2 and SARS? This study will find all those queries. Here, all protein sequences of SARS-CoV-2 and SARS are retrieved from the database to check their physicochemical, evolutionary and structural properties. Results showed that, charged residues are playing a key role in SARS-CoV-2 evolution. SARS-CoV-2 increases its polarity by the help of charged residues, not by the polar residues. Their divergence is also strictly restricted. Induction of salt bridges with their high energies makes it very stable in any extreme conditions. Microenvironment residues also play a very crucial role in its stability. Mostly residues are favorable and contribute high energies. These microenvironment residues help in protein engineering to reduce its stability and make them week. This comparative study will help to understand the evolution from SARS to SARS-CoV-2.

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PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins

Cited by 2 publications

References 10 publications

Salt-Bridges in the Microenvironment of Stable Protein Structures

Salt-Bridges in the Microenvironment of Stable Protein Structures

Comparative physicochemical and evolutionary study of SARS-CoV-2 and SARS with special reference to salt bridge and their microenvironment: A plausible explanation for divergency, stability and severity of SARS-CoV-2

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