Do homologous thermophilic-mesophilic proteins exhibit similar structures and dynamics at optimal growth temperatures? A molecular dynamics simulation study

Published in: Journal, Article, Volume : 53, Issue : 2, Pages : 423-434

DOI : 10.1021/ci300474h

Author : Basu, Sohini; Sen, Srikanta

Abstract : Structure and dynamics both are known to be important for the activity of a protein. A fundamental question is whether a thermophilic protein and its mesophilic homolog exhibit similar dynamics at their resp. optimal growth temperatures Here, the authors addressed this question by performing mol. dynamics (MD) simulations of a natural mesophilic-thermophilic homolog pair at their resp. optimal growth temperatures to compare their structural, dynamical, and solvent properties. The proteins chosen were the mesophilic cold-shock protein of Bacillus subtilis and the thermophilic cold-shock protein of B. caldolyticus with resp. optimal growth temperatures at 35.0 and 72.0°. The MD simulations were done in explicit aqueous solvent under periodic boundary and constant pressure and temperature (CPT) conditions and continued for 10.0 ns using the same protocol for the 2 proteins, excepting the temperatures The trajectories were analyzed to compare the properties of the 2 proteins. The results indicated that the dynamical behaviors of the 2 proteins at the resp. optimal growth temperatures were remarkably similar. For the common residues in the thermophilic protein, the rms fluctuations had a general trend to be slightly higher compared to that in the mesophilic counterpart. Lindemann parameter values indicated that only a few residues exhibited solid-like dynamics while the protein as a whole appeared as a molten globule in each case. Interestingly, the water-water interaction was found to be strikingly similar in spite of the difference in temperatures while, the protein-water interaction was significantly different in the 2 simulations.

Conjugate addition of indoles and pyrroles to dihydronitronaphthalenes in water: synthesis of 3,4-fused tetrahydro-β-carbolines

Published in: Journal, Volume : 2013, Issue : 4, Pages : 772-780

DOI : 10.1002/ejoc.201201288

Author : Malhotra, Rajesh; Ghosh, Rajib; Dey, Tushar K.; Chakrabarti, Sagar; Ghosh, Amit; Dutta, Swarup; Asijaa, Sonika; Roy, Subho; Dutta, Shantanu; Basu, Sourav; Hajra, Saumen

Abstract : A catalyst-free conjugate addition of indoles and pyrroles to 1,2-dihydro-3-nitronaphthalenes in water has been developed. A variety of indoles containing electron-rich and -deficient functional groups including aza-indoles and pyrroles reacted smoothly with a number of dihydro-3-nitronaphthalenes, especially bromo derivatives For structural elaboration, the bromo functionality (dihydronitronaphthalene unit as well as indolyl unit) of the addition products was utilized for Suzuki coupling reactions and provided moderate to good yields of the desired coupling compounds The utility of the method was further demonstrated by the synthesis of 3,4-fused tetrahydro-β-carbolines, a new class of compounds, from the addition products through reduction of the nitro group to the amine and subsequent Pictet-Spengler cyclization.

Designing of a fluoride selective receptor through molecular orbital engineering

Published in: Journal, Volume : 1027, Pages : 167-174

DOI : 10.1016/j.molstruc.2012.06.020

Author : Mishra, Rakesh K.; Kumar, Virendra; Diwan, Uzra; Upadhyay, K. K.; Roy Chowdhury, P. K.

Abstract : The stepwise substitution of appropriate groups over the 3-[(2,4-dinitro-phenyl)-hydrazono]-butyric acid Et ester (R3) lead receptor R1 which showed selectivity towards fluoride in DMSO. The UV-vis and 1H NMR titration studies revealed the details of the binding between receptor R1 and fluoride. The receptor R1 also recognized fluoride in a toothpaste solution to as low as 50 ppm. The theor. simulations of recognition event at D. Functional Theory (DFT) level using B3LYP/6-31G**t basis set and polarizable continuum model (PCM) approach lead a semi-quant. match with the exptl. results.

Rhodium-catalyzed enantioselective conjugate addition of arylboronic acids to dihydronitronaphthalenes

Published in: Journal, Volume : 354, Issue : 13, Pages : 2433-2437, S2433/1-S2433/39

DOI : 10.1002/adsc.201200241

Author : Hajra, Saumen; Ghosh, Rajib; Chakrabarti, Sagar; Ghosh, Amit; Dutta, Swarup; Dey, Tushar K.; Malhotra, Rajesh; Asijaa, Sonika; Roy, Subho; Dutta, Shantanu; Basu, Sourav

Abstract : A highly enantioselective (up to 91% ee) rhodium-catalyzed asym. addition of arylboronic acids has been achieved leading to the challenging dihydro-3-nitronaphthalenes using one equivalent of phosphoramidite ligand to rhodium catalyst. A concise formal asym. synthesis of the dopamine D1 agonist, dihydrexidine was accomplished using the method.

Benzimidazolium-based simple host for fluorometric sensing of H2PO4-, F-, PO43- and AMP under different conditions

Published in: Journal, Volume : 52, Issue : 39, Pages : 5098-5103

DOI : 10.1016/j.tetlet.2011.07.110

Author : Ghosh, Kumaresh; Kar, Debasis; Chowdhury, Purnendu Roy

Abstract : Pyrene appended benzimidazolium-based simple cleft (I) has been synthesized. The open cleft of I distinguishes H2PO4- and F- selectively by showing binding induced different emission characteristics in CH3CN. The chemosensor I also functions in aqueous CH3CN and shows marked change in emission in the presence of sodium phosphate at pH 6.5 and AMP at pH 7.3. Binding studies have been carried out using fluorescence, UV-vis and 1H NMR spectroscopic techniques.

Asymmetric synthesis of a dopamine D1 agonist, dihydrexidine from D-serine

Published in: Journal, Volume : 22, Issue : 14-15, Pages : 1522-1529

DOI : 10.1016/j.tetasy.2011.08.014

Author : Malhotra, Rajesh; Ghosh, Amit; Ghosh, Rajib; Chakrabarti, Sagar; Dutta, Swarup; Dey, Tushar K.; Roy, Subho; Basu, Sourav; Hajra, Saumen

Abstract : A scalable asym. synthesis of trans-2-amino-6,7-dimethoxy-1-phenyltetralin and its N-nosyl derivative have been achieved from Garner aldehyde derived from easily available D-serine using a stereoselective PhMgBr addition, Wittig reaction and TFA-mediated Friedel-Crafts cyclization as the key steps. The synthesis of dihydrexidine is accomplished from the N-nosyl-2-amino-1-phenyltetralin.

Predicting hERG activities of compounds from their 3D structures: Development and evaluation of a global descriptors based QSAR model

Published in: Journal, Article, Volume : 46, Issue : 2, Pages : 618-630

DOI : 10.1016/j.ejmech.2010.11.042

Author : Sinha, Nandita; Sen, Srikanta

Abstract : A QSAR based predictive model of hERG activity in terms of global descriptors’ has been developed and evaluated. The QSAR was developed by training 77 compounds covering a wide range of activities and was validated based on an external test set of 80 compounds using neural network method. Statistical parameters and examination of enrichment factor indicated the effectiveness of the present model. Randomization test demonstrated the robustness of the model and cross-validation test further validated the QSAR. Domain of applicability test indicated to the high degree of reliability of the predicted results. Satisfactory performance in classifying compounds into active’ and inactive’ groups was also obtained. The cases where the QSAR failed, the possible sources of errors have been discussed.

Discovery of novel quinolinone adenosine A2B antagonists

Published in: Journal, Article, Volume : 20, Issue : 24, Pages : 7414-7420

DOI : 10.1016/j.bmcl.2010.10.030

Author : McGuinness, Brian F.; Ho, Koc-Kan; Stauffer, Tara M.; Rokosz, Laura L.; Mannava, Neelima; Kultgen, Steven G.; Saionz, Kurt; Klon, Anthony; Chen, Weiqing; Desai, Hema; Rogers, W. Lynn; Webb, Maria; Yin, Juxing; Jiang, Yan; Li, Tailong; Yan, Hao; Jing, Konghua; Zhang, Shengting; Majumdar, Kanak Kanti; Srivastava, Vikash; Saha, Samiran

Abstract : A novel series of quinolinone-based adenosine A2B receptor antagonists was identified via high throughput screening of an encoded combinatorial compound collection. Synthesis and assay of a series of analogs highlighted essential structural features of the initial hit. Optimization resulted in an A2B antagonist (2i, I) which exhibited potent activity in a cAMP accumulation assay (5.1 nM) and an IL-8 release assay (0.4 nM).

A coumarin based ICT probe for fluoride in aqueous medium with its real application

Published in: Journal, Article, Research Support, Non-U.S. Gov’t, Volume : 82, Issue : 1, Pages : 312-318

DOI : 10.1016/j.talanta.2010.04.041

Author : Upadhyay, K. K.; Mishra, Rakesh K.; Kumar, Virendra; Chowdhury, P. K. Roy

Abstract : A new coumarin based hydrazone (receptor 1) synthesized by modifying one of our earlier reported receptor detected fluoride ion selectively through naked eye in aqueous DMSO (5:95, volume/volume). It was also able to detect fluoride through naked eye in a toothpaste sample. The addition of 1 equivalent of fluoride as its tetrabutylammonium salt to the 5 × 10-5 M aqueous DMSO solution of the receptor 1 produced red color while the similar addition of acetate produced faint pink color. The dihydrogen phosphate and a variety of other anions were not able to produce any significant color change with receptor 1 under similar exptl. conditions. The corresponding UV-vis measurements showed a bathochromic shifting of 455 nm band of receptor 1 to 514 and 484 nm for fluoride and acetate, resp. The non-linear fittings of corresponding UV-vis titration data in 1:1 binding equation yielded association constants in 105:1 ratio for fluoride and acetate, resp. The 1H NMR titrations studies shade further light on their mode of binding with receptor 1. The quantum mech. calculations through time dependant d. functional theory (TD-DFT) using basis set b3lyp/6-311g** supported our exptl. findings nicely.

Turning a Mesophilic Protein into a Thermophilic One: A Computational Approach Based on 3D Structural Features

Published in: Journal, Article, Volume : 49, Issue : 7, Pages : 1741-1750

DOI : 10.1021/ci900183m

Author : Basu, Sohini; Sen, Srikanta

Abstract : In spite of considerable improvement of our understanding of factors responsible for protein thermostability, rational designing of thermostable variants of mesophilic proteins is not yet fully established. The present paper describes an effective computational strategy that we have developed to identify the most suitable mutations converting a chosen mesophilic protein into a thermophilic one starting from its 3D structure. The approach is based on the concept that stabilization of several surface residues should enhance the global stability of the protein. The method relies on the estimation of electrostatic and van der Waals interactions in computing the interaction among the side chains of individual residues and the rest of the protein. The polar or charged residues whose side chains interact weakly with the rest of the original protein are identified first. Then, for each such identified residue (A), another residue (B) in its spatial vicinity is identified. The side chain of the residue (B) is then replaced by a suitable conformer of a residue that is electrostatically complementary to the residue (A) to enhance local interactions and hence the stability of the protein. The steric effect is taken care of through van der Waals interactions. We reject the mutations that improve interactions only locally along the sequence as it is unlikely to enhance the global stability of the 3D architecture. We use the difference in self-energies (ΔEself) as a measure of the stability difference between the original and its mutant variant. This paper presents two test cases with demonstration of the enhanced stability of such mutated proteins and validates the strategy by considering five exptl. known thermophilic-mesophilic protein pairs.