Interaction of an Antituberculosis Drug with a Nanoscopic Macromolecular Assembly: Temperature-Dependent Förster Resonance Energy Transfer Studies on Rifampicin in an Anionic Sodium Dodecyl Sulfate Micelle

In this contribution, we report studies on the nature of binding of a potent antituberculosis drug, Rifampicin (RF) with a model drug delivery system, sodium dodecyl sulfate (SDS) micelle. Temperature dependent dynamic light scattering (DLS), conductometry, and circular dichroism (CD) spectroscopy have been employed to study the binding interaction of the drug with the micelle. The absorption spectrum of the drug RF in the visible region has been employed to study Förster resonance energy transfer (FRET) from another fluorescent drug Hoechst 33258 (H33258), bound to the micelle. Picosecond-resolved FRET studies at room temperature confirm the simultaneous binding of the two drugs to the micelle and the distance between the donor−acceptor pair is found to be 34 Å. The temperature dependent FRET study also confirms that the location and efficiency of drug binding to the micelle changes significantly at the elevated temperature. The energy transfer efficiency of the donor H33258, as measured from time-resolved studies, decreases significantly from 76% at 20 °C to 60% at 55 °C. This reveals detachment of some amount of the drug molecules from the micelles and increased donor−acceptor distance at elevated temperatures. The estimated donor−acceptor distance increases from a value of 33 Å at 20 °C to 37 Å at 55 °C. The picosecond resolved FRET studies on a synthesized DNA bound H33258 in RF solution have been performed to explore the interaction between the two. Our studies are expected to find relevance in the exploration of a potential vehicle for the vital drug rifampicin

Orienting Macromolecule At The Air - Water Interface : DNA-Protein Interaction On Langmuir Films

The Langmuir – Blodgett (LB) technique is about forming insoluble monolayer on the surface of aqueous solution and recently, it has emerged as one of the best method to study floating monolayer at the air – water interface. It has gained popularity after the use of monolayer with chemical complexes as well as biological species, and recently it has been used for the formation of biosensors. Langmuir monolayer arrays the amphiphilic molecules in a fashion where the hydrophobic part points towards the air and the hydrophilic group remains in contact with the aqueous subphase. Due to this property of Langmuir monolayer to orient the molecules at the air – water interface in a particular fashion, it can successfully serve as a template for two – dimensional reactions with restricted freedom. Hence, Langmuir monolayer has been extensively employed to study chemical and biological reactions at the air – water interface. To understand the behavior of Langmuir monolayer, surface pressure – molecular area (P – A) isotherms are studied as these P – A isotherms illustrate general conditions regarding the phase behavior of the two-dimensional Langmuir monolayer. Any change occurring due to the alignment of aliphatic molecules forming the monolayer is reflected by the change in P – A isotherms, which is known as phase transition. The phase transition is the most important element of the P – A isotherms with a characteristic signature of a plateau region in the isotherms. This phase transition point changes with the change of certain external parameters such as temperature, pH, and ionic strength, and as a result gives general information regarding the phase transition behavior. Therefore, with the little change of external parameters, the arrangement of the molecules in the monolayer also changes, which is reflected in the change in the nature of the isotherms. Thus, the system can, in principle, be used to define several physical parameters associated with it. On account of the property of Langmuir monolayer to orient the molecules at the air – water interface with restricted mobility and due to their condensed nature known as solid like phase, it closely mimics the situation inside a biological cell. Hence, we wanted to test whether an artificial nucleus can be generated at LB films. This can be achieved by immobilizing DNA or protein at the air – water interface and then by promoting their biological properties through macromolecular recognition. Here, immobilization of a macromolecule of biological relevance, its interaction with another component of a cell and extracting the thermodynamic parameters utilizing the LB technique will be of significance. This thesis embodies the immobilization of some biologically important proteins then follows their activity as well as DNA recognition properties at the air – water interface. A set of equations are derived here for the two dimensional Langmuir monolayer, which are used to calculate the thermodynamics of the system under study. Chapter 1 outlines the information about Langmuir monolayer and LB films. It sketches the historical background of the Langmuir monolayer and also elucidates the theory behind the same. This chapter cites the technical details of formation of Langmuir monolayer and LB films viś – a – viś other methods available for the fabrication of monomolecular films. It adequately discusses the functional LB films and their utilization for various different purposes. Finally, the role of metal ions in the LB films and in immobilizing biological macromolecules is discussed. Chapter 2 discusses the different techniques employed to perform the experiments described in this thesis. It includes the purification methods for the different proteins and DNA; the details of formation of Langmuir monolayer and fabrication of LB films. This chapter also describes the various techniques used for the characterization of the LB films, i.e Atomic Force Microscopy (AFM) and Fourier Transform Infrared (FTIR) spectroscopy. In Chapter 3, immobilization and imaging of protein molecules and protein DNA complexes on a LB substrate have been explored. Firstly, we describe the preparation of a Ni (II) – arachidate (NiA) monolayer and its characterization through P – A isotherm on a LB trough. Then, recombinant RNA polymerase from Escherichia coli, where the largest subunit was replaced with the same gene having a series of histidine amino acids at the C-terminus end of the protein, was immobilized over the NiA monolayer through a Ni (II) – histidine interaction. A single molecule of RNA polymerase (RNAP) could be seen through intermittent-contact AFM. Under the condition of the formation of the LB monolayer, the enzyme molecules were arrayed and transcriptionally active. Interestingly, they could pick up sequence specific DNA molecules from the subphase in an oriented fashion. In Chapter 4, the interaction between NiA and histidine tagged RNAP (HisRNAP), and RNAP and DNA were studied. LB films of Arachidic acid – NiA, NiA -HisRNAP and NiA – HisRNAP – DNA with different mole fractions were fabricated systematically. P -A isotherms were registered, and the excess Gibbs energy of mixing was calculated. The LB films were then deposited on solid supports for FTIR spectroscopic measurements. The FTIR spectra revealed the change in the amount of incorporated Ni (II) ions into the AA monolayer with the change in pH. The increase in mole fraction of RNAP and DNA in the NiA and NiA – RNAP monolayer, respectively, with their increasing concentration in the subphase are also noticed. The system developed here is robust and can be utilized to follow macromolecular interactions. In chapter 5, the Langmuir monolayer has been utilized to array a protein, Dps, specific for Fe (II) and non-specific for DNA. Dps from Mycobacterium smegmatis is known to have a cage like structure, exists in two oligomeric states, trimer and dodecamer, and can accommodate Fe (II) ions in its internal cavity. In addition, it converts Fe (II) to Fe (III), both in trimeric and dodecameric form, whereas the latter species is specific for non-specific DNA binding. We demonstrate here that, histidine tagged Dps in both oligomeric states can be immobilized on NiA LB films, where both ferroxidation and DNA binding ability remained unaffected in the ordered protein assembly. Interestingly, when Fe (II) – arachidate was used to generate a LB layer instead of NiA, Dps protein not only recognizes Fe (II) ion in the monolayer, it also converts it to Fe (III) ion in a time dependent fashion. However, once Fe (III) – Dps complex is formed and arrayed on LB monolayers, it remains very stable

Macromolecular recognition at the air-water interface: application of Langmuir-Blodgett technique

The proximate aim of this review is to investigate the specific interaction between two macromolecules, either two complementary strands of DNA or the binding of DNA with a protein. Although a lot of experiments have been done to address these issues, our aim here is different. We either create a dense brush of DNA chains at the air–water interface or orient a large protein, like RNA polymerase, such that they are amenable for specific interaction at the surface. The advantage of our system is that the macromolecules are stretched, oriented parallel to each other, and their concentrations can be made similar to these encountered in real nuclei. In this way we plan to construct an ‘artificial nucleus’. Other methods adopted so far can check for the possibility of collective behaviour and the effect of chain elongation or compaction. We have used Langmuir– Blodgett technique for the same and extensively performed FTIR and AFM experiments to monitor the L–B surface. Each macromolecule has been attached by one of its extremities to a hydrophobic buoy to keep it at the interface. Detailed thermodynamic analysis results in some interesting conclusions

Macromolecular recognition at the air-water interface: application of Langmuir-Blodgett technique

The proximate aim of this review is to investigate the specific interaction between two macromolecules, either two complementary strands of DNA or the binding of DNA with a protein. Although a lot of experiments have been done to address these issues, our aim here is different. We either create a dense brush of DNA chains at the air-water interface or orient a large protein, like RNA polymerase, such that they are amenable for specific interaction at the surface. The advantage of our system is that the macromolecules are stretched, oriented parallel to each other, and their concentrations can be made similar to these encountered in real nuclei. In this way we plan to construct an 'artificial nucleus'. Other methods adopted so far can check for the possibility of collective behaviour and the effect of chain elongation or compaction. We have used Langmuir Blodgett technique for the same and extensively performed FTIR and AFM experiments to monitor the L-B surface. Each macromolecule has been attached by one of its extremities to a hydrophobic buoy to keep it at the interface. Detailed thermodynamic analysis results in some interesting conclusions

Thermodynamic and spectroscopic studies on the nickel arachidate-RNA polymerase Langmuir-Blodgett monolayer

The Langmuir-Blodgett (LB) monolayers offer a unique system to study molecular interaction at the air-water interface with reduced dimensionality. In order to develop this further to follow macromolecular interactions at equilibrium, we first characterized the Ni (II)-arachidate (NiA) monolayer at varying conditions. Subsequently, the interaction between NiA and histidine-tagged RNA polymerase (HisRNAP) were also studied. LB films of arachidic acid-NiA and NiA-RNAP with different mole fractions were fabricated systematically. Surface pressure versus area per molecule (P-A) isotherms were registered, and the excess Gibbs energy of mixing was calculated. The LB films were then deposited on solid supports for Fourier transform infrared (FTIR) spectroscopic measurements. The FTIR spectra revealed the change in the amount of incorporated Ni (II) ions into the arachidic acid monolayer with the change in pH and the increasing mole fraction of RNAP in the NiA monolayer with its increasing concentration in the subphase. The system developed here seems to be robust and can be utilized to follow macromolecular interactions

Thermodynamic and Spectroscopic Studies on the Nickel Arachidate-RNA Polymerase Langmuir-Blodgett Monolayer

The Langmuir-Blodgett (LB) monolayers offer a unique system to study molecular interaction at the air-water interface with reduced dimensionality. In order to develop this further to follow macromolecular interactions at equilibrium, we first characterized the Ni (II)-arachidate (NiA) monolayer at varying conditions. Subsequently, the interaction between NiA and histidine-tagged RNA polymerase (HisRNAP) were also studied. LB films of arachidic acid-NiA and NiA-RNAP with different mole fractions were fabricated systematically. Surface pressure versus area per molecule (P-A) isotherms were registered, and the excess Gibbs energy of mixing was calculated. The LB films were then deposited on solid supports for Fourier transform infrared (FTIR) spectroscopic measurements. The FTIR spectra revealed the change in the amount of incorporated Ni (II) ions into the arachidic acid monolayer with the change in pH and the increasing mole fraction of RNAP in the NiA monolayer with its increasing concentration in the subphase. The system developed here seems to be robust and can be utilized to follow macromolecular interactions

Sequence Specific Interaction between Promoter DNA and Escherichia coli RNA Polymerase: Comparative Thermodynamic Analysis with One Immobilized Partner

Sequence specific interaction between DNA and protein molecules has been a subject of active investigation for decades now. Here, we have chosen single promoter containing bacteriophage Delta D-III T7 DNA and Escherichia coli RNA polymerase and followed their recognition at the air-water interface by using the surface plasmon resonance (SPR) technique, where the movement of one of the reacting species is restricted by way of arraying them on an immobilized support. For the Langmuir monolayer studies, we used a RNA polymerase with a histidine tag attached to one of its subunits, thus making it an xcellent substrate for Ni(II) ions, while the SPR Studies were done using biotin-labeled DNA immobilized on a streptavidin-coated chip. Detailed analysis of the thermodynamic parameters as a function of concentration and temperature revealed that the interaction of RNA polymerase with T7 DNA is largely entropy driven (83 (+/- 12) kcal mol(-1)) with a positive enthalpy of 13.6 (+/- 3.6) kcal mol(-1), The free energy of reaction determined by SPR and Langmuir-Blodgett technique was -11 (+/- 2) and -15.6 kcal mol(-1), respectively. The ability of these methods to retain the specificity of the recognition process was also established

Simultaneous binding of anti-tuberculosis and anti-thrombosis drugs to a human transporter protein: A FRET study

Although rifampicin (Rf) is one of the most effective antibiotics against infection caused by Mycobacterium tuberculosis, interaction of the drug with universal carrier protein in human blood plasma is not fully understood. Reduction of medicinal efficacy of other drugs, including anti-thrombosis drug warfarin (Wf), to the patients on Rf therapy also needs molecular understanding. In the present work we have studied interaction of Rf with one of the model carrier protein (human serum albumin). By using circular dichroism (CD) spectroscopy we have characterized the change in the secondary structure of the protein. The consequence of the simultaneous binding of the two drugs, Rf and Wf, on the structure of the protein has also been explored. Picosecond resolved Förster resonance energy transfer (FRET) from Wf to Rf explores possible binding sites of the anti-tuberculosis drug on the protein. In this report, we have discussed the potential problem of using the single tryptophan of the protein (Trp 214) as energy donor in FRET experiment for the characterization of the binding site of the drug Rf on the protein

Langmuir Monolayer as a Tool toward Visualization of a Specific DNA-Protein Complex

Immobilization and imaging of protein molecules and protein-DNAcomplexes on a Langmuir-Blodgett (LB) substrate have been explored here. We have prepared a nickel-arachidate (NiA) monolayer and characterized it through pressure-area isotherm on a LB trough. Recombinant RNA polymerase from Escherichia coli, where the largest subunit was replaced with the same gene having a series of histidine amino acids at the C-terminus end of the protein, was immobilized over the Ni-arachidate monolayer through a Ni(II)-histidine interaction. A single molecule of RNA polymerase could be seen through intermittent-contact atomic force microscopy (AFM). Under the condition of the formation of the LB monolayer, the enzyme molecules were arrayed and transcriptionally active. Interestingly, they could pick up sequence specificDNAmolecules from the subphase in an oriented fashion.Onthe other hand, preformed RNA polymerase Ni(II)-arachidate monolayers bound DNA haphazardly when no surface pressure was employed