ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2

Nayek, Arnab; Gupta, Parth Sarthi Sen; Banerjee, Sumanta; Sur, Vishma Pratap; Seth, Pratyay; Das, Sunit; Islam, Rifat Nawaz Ul; Bandyopadhyay, Amal Kumar

doi:10.6026/97320630011413

Cited by 12 publications

(18 citation statements)

References 9 publications

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“…Salt‐bridge energy calculation by computational approaches was observed by experimental method . We have followed the former procedure as constructed by Hendsch and Tidor (1994) along with ADSBET2 . The total electrostatic free energy (∆∆ G net ) can be decomposed into three energy terms: (a) ∆∆ G dslv is the energy difference caused by desolvation of charged residues forming salt‐bridge in the folded state of protein.…”

Section: Methodsmentioning

confidence: 70%

“…While the PBE and its solver method is reliable for the computation of direct and indirect component energy terms and hence the net energetics of ion‐pairs, it is an approximate method. Computation either at low pH (<1.0) or without mobile ion concentration may produce erroneous results due to high charge density situations within protein molecules .…”

Section: Discussionmentioning

confidence: 99%

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Comparative studies on ion‐pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya

2020

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Salt‐bridges play a unique role in the structural and functional stability of proteins, especially under harsh environments. How these salt‐bridges contribute to the overall thermodynamic stability of protein structure and function across different domains of life is elusive still date. To address the issue, statistical analyses on the energies of salt‐bridges, involved in proteins' structure and function, are performed across three domains of life, that is, archaea, eubacteria, and eukarya. Results show that although the majority of salt‐bridges are stable and conserved, yet the stability of archaeal proteins (∆∆Gnet = −5.06 ± 3.8) is much more than that of eubacteria (∆∆Gnet = −3.7 ± 2.9) and eukarya (∆∆Gnet = −3.54 ± 3.1). Unlike earlier study with archaea, in eukarya and eubacteria, not all buried salt‐bridge in our dataset are stable. Buried salt‐bridges play surprising role in protein stability, whose variations are clearly observed among these domains. Greater desolvation penalty of buried salt‐bridges is compensated by stable network of salt‐bridges apart from equal contribution of bridge and background energy terms. On the basis proteins' secondary structure, topology, and evolution, our observation shows that salt‐bridges when present closer to each other in sequence tend to form a greater number. Overall, our comparative study provides insight into the role of specific electrostatic interactions in proteins from different domains of life, which we hope, would be useful for protein engineering and bioinformatics study.

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Section: Methodsmentioning

confidence: 70%

Section: Discussionmentioning

confidence: 99%

Comparative studies on ion‐pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya

2020

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“…Program is written in AWK programming language, which can preferably run in any C shell UNIX prompt including CYGWIN 32 bit and also be made work in B shell LINUX and WINDOWS environment. Presently we are actively engaged in developing web interface to integrate SBION2 and ADSBET2 [ 9 , 10 ] along with other related software tools of our laboratory [ 6 , 7 , 8 , 11 ] such that their availability could reach to all academic users within an integrated web service.…”

Section: Methodsmentioning

confidence: 99%

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

Islam

Pss

et al. 2018

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Residues in allelic positions, in the local segment of aligned sequences of proteins show wide variations. Here, we describe PROPAB that computes the propensity tables for helix, strand and coil types from multiple 3D structure files following ab initio statistical procedure. It also classifies them in range specific and chain specific manners. It further computes percentage composition and physicochemical properties along with residues propensities. It also prepares FASTA files for different segments (helix, strand and coil) in the exact order that they follow in the sequence. Representative analyses on orthologous (homologous across species) proteins demonstrate wide segmental variations of physicochemical properties. Such variations provide insights to relate the adaptation of these proteins in a given functional constraint under diverse environmental conditions. Thus, the program finds applications in the structural and evolutionary analysis of proteins.Availability:PROPAB is freely available at http://sourceforge.net/projects/propab/for worldwide user.

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“…The net-energy (δδgnet) of the salt-bridge in the computation method depends on three component terms namely δδgdslv, δδgbrd and δδgbac i.e. The folded and unfolded states of the protein are considered to compute δδgdslv, but only the first state is used for the other two [26,27,28,29]. The desolvation of the positive and negative charges of the salt-bridge is independent, so they are computed separately.…”

Section: Salt-bridge Model and Energetic Computationmentioning

confidence: 99%

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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ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2

Cited by 12 publications

References 9 publications

Comparative studies on ion‐pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya

Comparative studies on ion‐pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya

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

Salt-Bridges in the Microenvironment of Stable Protein Structures

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