SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files

Gupta, Parth Sarthi Sen; Mondal, Sudipta; Mondal, Buddhadev; Islam, Rifat Nawaz Ul; Banerjee, Sumanta; Bandyopadhyay, Amal Kumar

doi:10.6026/97320630010164

Cited by 20 publications

(29 citation statements)

References 8 publications

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“…The salt bridges formed between two oppositely charged side-chain atoms, (i.e., basic and acidic amino acids) within a distance of 4 Å and contributing to the stability and electrostatics of the protein complex was calculated using the SBION program, 47 and intermolecular salt bridges were then extracted such that the oppositely charged atoms are from two different subunits.…”

Section: Intermolecular Salt Bridges Calculationmentioning

confidence: 99%

Linking structural features of protein complexes and biological function

2015

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Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r 5 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions.

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Section: Intermolecular Salt Bridges Calculationmentioning

confidence: 99%

Linking structural features of protein complexes and biological function

2015

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“…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: 78%

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

Bandyopadhyay¹

2015

Biochem Anal Biochem

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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.

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“…SBION2, like our earlier developments [ 1 , 4 ], is meant for automated analysis of single or multiple input(s). The program possesses many new features over the existing ones.…”

Section: Methodsmentioning

confidence: 99%

“…Salt-bridges ( SBs ) ( Figure 1C ), bonds between oppositely charged side chain atoms of acidic (acceptor atoms, red residue in Figure 1C ) and basic (donor atoms, blue residues in Figure 1C ) residues that are within 4~ distance, contribute to the overall stability of native state of proteins [ 1 ]. Software for determination of atomic intra- and inter-chain SBs and their secondary structural distribution are now available for single input of user choice per run [ 2 ] and for multiple structure files per run along with additional details on networked SB and missing residues information [ 1 ]. However, further development is sought for details on residue specific SB (but not atomic ones as above) as to whether it is in core or surface of protein, isolated or networked, single or multiple (bonds ≥ 2) bonded, hydrogen or non hydrogen bonded, local or non-local (if local, i→(i+n) typing) and intra- or inter-helical/strand/coil.…”

Section: Introductionmentioning

confidence: 99%

“…basic residue is at N-terminal [orientation-I] or acidic residue is at Nterminal [Orientation-II]) would be useful in understanding structural stability as well as packing [ 3 ]. In this end SBION2 has been the first of its kind which not only display all the above details in systematic manner along with others [ 1 ] but also store similar kind of data in excel format for comprehensive post run statistical analyses involving a large number of structural files.…”

Section: Introductionmentioning

confidence: 99%

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

Gupta¹,

Nayek²,

Banerjee³

et al. 2015

Bioinformation

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Specific electrostatics (i.e. salt-bridge) includes both local and non-local interactions that contribute to the overall stability of proteins. It has been shown that a salt-bridge could either be buried or exposed, networked or isolated, hydrogen-bonded or nonhydrogen bonded, in secondary-structure or in coil, formed by single or multiple bonds. Further it could also participates either in intra- or inter-dipole interactions with preference in orientation either for basic residue at N-terminal (orientation-I) or acidic residue at N-terminal (orientation-II). In this context SBION2 is unique in that it reports above mentioned binary items in excel format along with details on intra and inter-dipole interactions and orientations. These results are suitable for post run statistical analyses involving large datasets. Reports are also made on protein-protein interactions, intervening residue distances and general residue specific salt-bridge details. A ready to use compact supplementary table is also produced. The program runs in three alternative modes. Each mode works on any number of structure files with any number of chains at any given atomic distance of ion-pair. Thus SBION2 provides intricate details on salt-bridges and finds application in structural bioinformatics.AvailabilitySBION2 is freely available at http://sourceforge.net/projects/sbion2/ for academic users

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SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files

Cited by 20 publications

References 8 publications

Linking structural features of protein complexes and biological function

Linking structural features of protein complexes and biological function

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

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

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