SBION2: Analyses of Salt Bridges from Multiple Structure Files, Version 2

Gupta, Parth Sarthi Sen; Nayek, Arnab; Banerjee, Sumanta; Seth, Pratyay; Das, Sunit; Sur, Vishma Pratap; Roy, Chittran; Bandyopadhyay, Amitabha

doi:10.6026/97320630011039

Cited by 17 publications

(26 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, contention of contribution of salt bridges in halo adaptation of HmFd was proposed to be due counterbalance effect of the former by [2Fe-2S]chromophore center [28]. However, this does not corroborate with a recent generalized theoretical studies on salt bridges of halophilic proteins [35][36][37]. Instead, as revealed in the atomic structure [28], a novel mode of stabilization was observed in that except the active site (Figure 1: AS) the entire surface of HmFd (Figure 1: S) is covered with cluster of negative charges along with the N-terminal hyper acidic domain (Figure 1: B) that are stabilized by H-bonding and dipole interactions contributed by tightly bound hydration shells [31].…”

Section: Role Of N-terminal Insertion Domain In Halo Halophilicmentioning

confidence: 80%

Stability of Halophilic Proteins in Hyper Saline Brine: [2Fe-2S] Ferredoxin as a Paradigm

Bandyopadhyay¹

2015

Biochem Anal Biochem

View full text Add to dashboard Cite

Apart from normal or mesophilic environment, organisms are found in extreme of salinity, and other hostile environments in the earth. Extreme halophiles thrive as pure culture in their natural environments of saturated salt as other microbes can't venture to grow. Over the evolution, these microorganism grew up with specialized transport-devices to solve the problem of osmoregulation. As a consequence whole of their biochemical machinery started functioning in this highly saline brine situation that mesophile cannot withstand. Intensive researches are thus carried out over the last fifty years to understand salt dependent properties of these proteins and enzymes. Ferredoxin is a small soluble protein that functions as electron carrier in decarboxylation reactions in cytoplasm in conjunction with an oxidoreductase. Two of its representatives from Halobacterium marismortui (HmFd) and Halobacterium salinarum (HsFd) are extensively studied. Atomic structures of HmFd and HsFd reveal that halo adaptation is largely mediated by a hyper acidic inserted domain of some 24 residues long at N-terminus region. By designed kinetics and thermodynamics experiments it was demonstrated that HsFd indeed adapted in high salt and requires ≥1.5M salt to retain its overall structural integrity. While non-specific electrostatic effect is operative at ≤0.25M salt, higher salt promote salt-bridge and hydrophobic stability. At intermediate salt where Hofmeister effects of specific ion interactions are operative, HsFd forms a hydrophobic collapsed intermediate whose structural properties differs from its native state in saturated salts. Thus intuitively, HsFd in its native state seems to entertain a post Hofmeister like effect in that wide modulation of tertiary interactions might occur.

show abstract

Section: Role Of N-terminal Insertion Domain In Halo Halophilicmentioning

confidence: 80%

Stability of Halophilic Proteins in Hyper Saline Brine: [2Fe-2S] Ferredoxin as a Paradigm

Bandyopadhyay¹

2015

Biochem Anal Biochem

View full text Add to dashboard Cite

show abstract

“…Within secondary structure of protein, the side chain‐side chain contacts were included: between i → i + 4, i → i + 3, i + 2, and i + 1 (Supporting Information Figure S1) for inter‐ or intra‐helical/strand/coil or inter‐helical/strand/coil. Analysis of all possible salt‐bridge interaction study was done by SBION2 …”

Section: Methodsmentioning

confidence: 99%

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

2020

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…If present, these are screened out and a new list ( Figure 1 - M2 ) is made, otherwise continue with the earlier list ( Figure 1 - M3 ). Such a design is adapted from earlier works [ 7 , 9 ]. Now the program enters into processing phase ( Figure 1 - P1 ).…”

Section: Methodsmentioning

confidence: 99%

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

Islam

Pss

et al. 2018

Bioinformation

Self Cite

View full text Add to dashboard Cite

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.

show abstract

SBION2: Analyses of Salt Bridges from Multiple Structure Files, Version 2

Cited by 17 publications

References 4 publications

Stability of Halophilic Proteins in Hyper Saline Brine: [2Fe-2S] Ferredoxin as a Paradigm

Stability of Halophilic Proteins in Hyper Saline Brine: [2Fe-2S] Ferredoxin as a Paradigm

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

Contact Info

Product

Resources

About