title: Salt-bridge energetics in halophilic proteins.
abstract: Halophilic proteins have greater abundance of acidic over basic and very low bulky hydrophobic residues. Classical electrostatic stabilization was suggested as the key determinant for halophilic adaptation of protein. However, contribution of specific electrostatic interactions (i.e. salt-bridges) to overall stability of halophilic proteins is yet to be understood. To understand this, we use Adaptive-Poison-Boltzmann-Solver Methods along with our home-built automation to workout net as well as associated component energy terms such as desolvation energy, bridge energy and background energy for 275 salt-bridges from 20 extremely halophilic proteins. We then perform extensive statistical analysis on general and energetic attributes on these salt-bridges. On average, 8 salt-bridges per 150 residues protein were observed which is almost twice than earlier report. Overall contributions of salt-bridges are -3.0 kcal mol-1. Majority (78%) of salt-bridges in our dataset are stable and conserved in nature. Although, average contributions of component energy terms are equal, their individual details vary greatly from one another indicating their sensitivity to local micro-environment. Notably, 35% of salt-bridges in our database are buried and stable. Greater desolvation penalty of these buried salt-bridges are counteracted by stable network salt-bridges apart from favorable equal contributions of bridge and background terms. Recruitment of extensive network salt-bridges (46%) with a net contribution of -5.0 kcal mol-1 per salt-bridge, seems to be a halophilic design wherein favorable average contribution of background term (-10 kcal mol-1) exceeds than that of bridge term (-7 kcal mol-1). Interiors of proteins from halophiles are seen to possess relatively higher abundance of charge and polar side chains than that of mesophiles which seems to be satisfied by cooperative network salt-bridges. Overall, our theoretical analyses provide insight into halophilic signature in its specific electrostatic interactions which we hope would help in protein engineering and bioinformatics studies.
authors.affiliation: The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India.
authors.forename: Arnab
authors.initials: A
authors.lastname: Nayek
authors.affiliation: The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India.
authors.forename: Parth Sarthi
authors.initials: PS
authors.lastname: Sen Gupta
authors.affiliation: The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India.
authors.forename: Shyamashree
authors.initials: S
authors.lastname: Banerjee
authors.affiliation: Department of Zoology, Burdwan Raj College, The University of Burdwan, Burdwan, West Bengal, India.
authors.forename: Buddhadev
authors.initials: B
authors.lastname: Mondal
authors.affiliation: The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India.
authors.forename: Amal K
authors.initials: AK
authors.lastname: Bandyopadhyay
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D006860:Hydrogen Bonding; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012492:Salts / Q000494:pharmacology*; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D011506:Proteins; D012492:Salts
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