Insights from the salt bridge analysis of malate dehydrogenase from H. salinarum and E.coli

Characterization and mechanism investigation of salt-activated methionine sulfoxide reductase A from halophiles

Halophiles, thriving in harsh saline environments, capture scientific interest due to their remarkable ability to prosper under extreme salinity. This study unveils the distinct salt-induced activation of methionine sulfoxide reductases (MsrA) from Halobacterium hubeiense, showcasing a significant enhancement in enzymatic activity across various salt concentrations ranging from 0.5 to 3.5 M. This contrasts sharply with the activity profiles of non-halophilic counterparts. Through comprehensive molecular dynamics simulations, we demonstrate that salt ions stabilize and compact the enzyme's structure, notably enhancing its substrate affinity. Mutagenesis analysis further confirms the essential role of salt bridges formed by the basic Arg168 residue in salt-induced activation. Mutating Arg168 to an acidic or neutral residue disrupts salt-induced activation, substantially reducing the enzyme activity under salt conditions. Our research provides evidence of salt-activated MsrA activity in halophiles, elucidating the molecular basis of halophilic enzyme activity in response to salts.

Underlying features for the enhanced electrostatic strength of the extremophilic malate dehydrogenase interface salt-bridge compared to the mesophilic one

Malate dehydrogenase (MDH) exists in multimeric form in normal and extreme solvent conditions where residues of the interface are involved in specific interactions. The interface salt-bridge (ISB) and its microenvironment (ME) residues may have a crucial role in the stability and specificity of the interface. To gain insight into this, we have analyzed 218 ISBs from 42 interfaces of 15 crystal structures along with their sequences. Comparative analyses demonstrate that the ISB strength is ∼30 times greater in extremophilic cases than that of the normal one. To this end, the interface residue propensity, ISB design and pair selection, and ME-residue's types, i.e., type-I and type-II, are seen to be intrinsically involved. Although Type-I is a common type, Type-II appears to be extremophile-specific, where the net ME-residue count is much lower with an excessive net ME-energy contribution, which seems to be a novel interface compaction strategy. Furthermore, the interface strength can be enhanced by selecting the desired mutant from the net-energy profile of all possible mutations of an unfavorable ME-residue. The study that applies to other similar systems finds applications in protein-protein interaction and protein engineering.Communicated by Ramaswamy H. Sarma.

One-Pot Purification and Immobilization of Phenylalanine Dehydrogenase from Bacillus nanhaiensi by Functional Reduced Graphene Oxide

The one-pot immobilization of halophilic phenylalanine dehydrogenase from marine microorganism with metal ions modified reduced graphene oxide (CRGO) material was studied. Phenylalanine dehydrogenase was from Bacillus nanhaiensi and expressed with a C-terminal His-tag. Investigation of CRGO, CRGO-PEI, CRCO-Mn, and CRGO-PEI-Mn for one-pot purification and immobilization of phenylalanine dehydrogenase from crude enzyme solution was carried out. Enzyme activity yield rate achieved 80.0% by immobilization with CRCO-Mn, and the loading capacity was 6.7 mg/mg. Manganese ion coordination greatly improved the selectivity of the CRGO for the target His-tagged enzyme. Furthermore, the effect of NaCl concentration on the immobilization was investigated, which the loading capacity of CRGO-PEI and CRGO-Mn-PEI was increased by 10.7% and 30.6% with 1 M NaCl, respectively. The adsorption curves of crude enzyme one-pot immobilized by CRGO-Mn and purified enzyme immobilized by CRGO-Mn were similar. Therefore, one-pot immobilization strategy is promising for industrial application with advantages such as high efficiency and low cost, which shorten the pipelines for enzyme discovery towards industrial applications through the establishing of marine enzyme collections.

Salt-bridges in the microenvironment of stable protein structures

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 4 Å away from positive and negative partners of salt-bridge and interact with them). MEs act as a determinant of net-energy due to the intrinsic features in 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 protein data bank (PDB) and a homology model (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 to develop thermo stable proteins with strong salt bridges.

Contributions of protein microenvironment in tannase industrial applicability: An in-silico comparative study of pathogenic and non-pathogenic bacterial tannase

Tannase is an inducible industrially important enzyme, produced by several microorganisms. A large number of bacteria have reported as tannase producers; however, some of them are pathogenic in nature. Therefore, it is quite uncertain whether the application of these tannase enzymes from such pathogenic bacteria is suitable for industries and human welfare. Till date, there is no clear evidence regarding which group of bacteria (non-pathogenic or pathogenic) is better suited for their application in the edge of industries with particular reference to the food industry. The present study is following the findings of the above queries. In this study, a large number of tannase protein sequences have been retrieved from the databases, including both non-pathogenic and pathogenic bacterial species. Physiochemical and evolutionary properties of those sequences have been evaluated. Results have shown that non-pathogenic bacterial tannase possesses a high number of acidic and basic amino acid residues as compared to their pathogenic counterparts. The acidic and basic amino acid residues of tannase provide unique microenvironment to it. In the other hand, the numbers of disorder forming residues are higher in tannase sequences of pathogenic bacteria. The study of tannase microenvironment leads in the formation of salt bridges, which finally favoring the stability and proper functioning of tannase. This is the first report of such observation on tannase enzyme using in silico approach. Study of the microenvironment concept will be helpful in protein engineering.