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Molecular Biology of Thermophilic and Psychrophilic Archaea
Published in Ajar Nath Yadav, Ali Asghar Rastegari, Neelam Yadav, Microbiomes of Extreme Environments, 2021
Chaitali Ghosh, Jitendra Singh Rathore
Salt-bridging is also an important feature of most thermophilic enzymes (Karshikoff and Ladenstein 2001). In the case of mesophiles, salt-bridging may destabilize proteins and hence hydrophobic interactions are more favourable (Hendsch and Tidor 1994). The entropic cost and desolvation penalty are generally associated with ion pairing found in salt bridges and are more easily overcome at higher temperatures (Chan et al. 2011). When these thermodynamic considerations are ignored, salt bridges are considered as a structurally stabilizing element and hence increase the thermal capacity of proteins using favourable charge-charge interactions. Biophysical studies of L30e showed that thermophilic ribosomal protein from Thermococcus celer produced a remarkable change in thermal capacity without causing major structural changes (Chan et al. 2011). In the site-directed mutagenesis approach where charged residues involved in salt-bridging are replaced with hydrophobic residues, results showed an increase in the heat capacity change of unfolding, ΔCp. One approach used by thermophiles to enhance the thermostability of their proteins is by lowering the ΔCp and uphold the natively folded structure over that of the unfolded one. This proves that favourable interactions of charged residues (salt bridges) are essential and in return they improve the thermal stability of proteins (Chan et al. 2011).
Nanostructured Cellular Biomolecules and Their Transformation in Context of Bionanotechnology
Published in Anil Kumar Anal, Bionanotechnology, 2018
Protein consists of α-l-amino acids linked by peptide bonds to form a polypeptide chain. At neutral pH, the amino group is positively charged, whereas the carboxyl group is negatively charged. Thus, N-terminal of protein remains positively charged and the C-terminal is negatively charged. Positively and negatively charged amino acids often form salt bridges, which may be important for the stabilization of the protein 3D structure; for example, proteins from thermophilic organisms often have an extensive network of salt bridges on their surface, which contributes to the thermos ability of these proteins. Inside the cell, under normal physiological conditions at a pH range of 6.8–7.4, amino group (−NH3+) and carboxyl group (−COO−) are ionized as they have pKa (negative base-10 logarithm of the acid dissociation constant) value around 9 and 3, respectively. The amino acids thus exist in dipolar ion condition with 0 net charges, which is known as zwitterions. Except glycine, in rest of amino acids, the α-carbon atom is asymmetric or chiral, because four different groups are bonded to it. These 19 chiral amino acids exist as stereoisomers (same molecular formula but different arrangement) and enantiomers (nonsuperimposable mirror image of stereoisomers) (Moran et al. 2012).
Atomistic simulation of hierarchical nanostructured materials for optical chemical sensing
Published in Alexander Bagaturyants, Vener Mikhail, Multiscale Modeling in Nanophotonics, 2017
Alexander Bagaturyants, Vener Mikhail
Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two- stranded β-sheet structure. NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations were localized [105]. These structures are stabilized by short N+-H . . . O bonds. Their relative stability depends on the force field used in MD simulations. The side-on structure is the most stable in terms of the OPLS-aa force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS-aa force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several shortliving species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm−1. It is caused by the asymmetric stretching vibrations of the N+–H⋯O fragment. These results suggest that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins [106].
Kinetic, thermodynamic parameters and in vitro digestion of tannase from Aspergillus tamarii URM 7115
Published in Chemical Engineering Communications, 2018
Amanda Reges de Sena, Tonny Cley Campos Leite, Talita Camila Evaristo da Silva Nascimento, Anna Carolina da Silva, Catiane S. Souza, Antônio Fernando de Mello Vaz, Keila Aparecida Moreira, Sandra Aparecida de Assis
The effect of substances on the enzymatic activity is shown in Table 7. The salts act as ion or salt bridges used to keep the conformation of the enzyme or to stabilize the binding between the substrate and enzyme complex. Cofactors are in general not required for tannase activity, but the divalent cations, such as magnesium, often stimulate the enzyme activity. Such response may be due to the contribution of several mechanisms such as the metal ion activation, which takes place through the modification of equilibrium constant of the enzyme reaction or through changes in the surface charge of the enzyme protein (Mukherjee and Banerjee, 2006). The study about the influence of monovalent (Na+ and K+) and divalent cations (Ca2+, Mg2+, and Mn2+) on tannase activity has shown that these cations had activating effect at concentration 5 × 10−3 mol/L. Fe2+ at concentration 1 × 10−3 mol/L was also able to enhance the activity. High salt-tolerant enzymes are essential for biotechnological processes dependent on salinity or osmotic pressure (Annamalai et al., 2014).
Protein a resin lifetime study: Evaluation of protein a resin performance with a model-based approach in continuous capture
Published in Preparative Biochemistry and Biotechnology, 2018
Ketki Behere, Bumjoon Cha, Seongkyu Yoon
On the one hand, Protein A leaching, resulting in Protein A ligands to be eluted with the product, is known to complicate the subsequent purification steps.[31,32] On the other hand, fouling which is the result of irreversible binding of product moieties, impurities, and nonspecific binding of aggregates is known for obstructing the access to Protein A ligands in the resin pores. The nonspecific binding is postulated to occur near the surface of the resin particle which further obstructs the access to the Protein A ligands within the pores, decreasing the overall life span of the column.[9,33] Use of harsh alkali conditions can also cause serious damage to the resin structure and function. In fact, sodium hydroxide (NaOH) has been identified as the primary cause of such alkali-based resin degradation.[8,34] NaOH is a widely accepted sanitizing agent in the biopharmaceutical industry due to its cost-effective sanitizing efficiency against viruses, bacteria, yeasts, endotoxins, etc.[34,35] Since NaOH acts by breaking down proteins, it is detrimental to the Protein A ligand. The hydroxyl (OH−) ions interact with the hydrophilic and positively charged side chains of the Protein A amino acids. The charged and polar side chains of the amino acids are displayed on the ligand surface in a solvent and hence are easily accessible. Hydrophilic amino acids such as lysine form salt bridges with the hydroxyl ions in caustic. Salt bridges are electrostatic interactions and hydrogen binding which provide conformational specificity to a protein. The salt bridges formed between caustic and lysine residues prevent the formation of geometric alignment of Protein A which is imperative to the antibody binding.[363738] Other polar amino acids, namely, arginine, glutamine, and histidine form hydrogen bonds with the caustic, wherein the amide group acts as a proton donor and the hydroxyl group (OH−) on the caustic acts as a proton acceptor.[39] The hydrogen on the amide group interacts electrostatically with the hydroxyl group on the caustic to form a hydrogen bond. Due to this hydrogen bond formation, the amide group is no longer available to bind to other hydrophilic groups on the protein, which would enable the desired conformation to bind to the antibody. Thus, the interaction between the stationary Protein A and free ionic species (OH−) leads to establishing a Donnan equilibrium, wherein the OH− ions form salt bridges and/or hydrogen bonds at the lysine, arginine, glutamine, and histidine residues.[40]