Modulating the structures and properties of biomembranes via permeation of small amphiphilic mole... more Modulating the structures and properties of biomembranes via permeation of small amphiphilic molecules is immensely important, having diverse applications in cell biology, biotechnology, and pharmaceuticals, because their physiochemical and biological interactions lead to new pathways for transdermal drug delivery and administration. In this work, we have elucidated the role of dimethyl sulfoxide (DMSO), broadly used as a penetration-enhancing agent and cryoprotective agent on model lipid membranes, using a combination of fluorescence microscopy and time-resolved fluorescence spectroscopy. Spatially resolved fluorescence lifetime imaging microscopy (FLIM) has been employed to unravel how the fluidity of the DMSO-induced bilayer regulates the structural alteration of the vesicles. Moreover, we have also shown that the dehydration effect of DMSO leads to weakening of the hydrogen bond between lipid headgroups and water molecules and results in faster solvation dynamics as demonstrated by femtosecond time-resolved fluorescence spectroscopy. It has been gleaned that the water dynamics becomes faster because bilayer rigidity decreases in the presence of DMSO, which is also supported by time-resolved rotational anisotropy measurements. The enhanced diffusivity and increased membrane fluidity in the presence of DMSO are further ratified at the single-molecule level through fluorescence correlation spectroscopy (FCS) measurements. Our results indicate that while the presence of DMSO significantly affects the 1,2-dimyristoyl-rac-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-rac-glycero-3-phosphatidylcholine (DPPC) bilayers, it has a weak effect on 1,2-dimyristoyl-sn-glycero-3-phospho-rac-glycerol (DMPG) vesicles, which might explain the preferential interaction of DMSO with the positively charged choline group present in DMPC and DPPC vesicles. The experimental findings have also been further verified with molecular dynamics simulation studies. Moreover, it has been observed that DMSO is likely to have a differential effect on heterogeneous bilayer membranes depending on the structure and composition of their headgroups. Our results illuminate the importance of probing the lipid structure and composition of cellular membranes in determining the effects of cryoprotective agents.
Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the c... more Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a polymer brush. We propose a mesoscopic model for the transport of a protein through the plug, that is general enough to cover both. The protein stretches the plug and creates a local deformation. The bubble so created (prtoein+deformation) executes random walk in the plug. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. Further, on using parameters appropriate for the brush, we find that the diffusion coefficient is much lower. Hence the gel model seems to be more likely explanation for the workings of the plug.
The correct interplay of interactions between protein, pigment and lipid molecules is highly rele... more The correct interplay of interactions between protein, pigment and lipid molecules is highly relevant for our understanding of the association behavior of the light harvesting complex (LHCII) of green plants. To cover the relevant time and length scales in this multicomponent system, a multi-scale simulation ansatz is employed that subsequently uses a classical all atomistic (AA) model to derive a suitable coarse grained (CG) model which can be backmapped into the AA resolution, aiming for a seamless conversion between two scales. Such an approach requires a faithful description of not only the protein and lipid components, but also the interaction functions for the indispensable pigment molecules, chlorophyll b and chlorophyll a (referred to as chl b/chl a). In this paper we develop a CG model for chl b and chl a in a dipalmitoylphosphatidyl choline (DPPC) bilayer system. The structural properties and the distribution behavior of chl within the lipid bilayer in the CG simulations are consistent with those of AA reference simulations. The non-bonded potentials are parameterized such that they fit to the thermodynamics based MARTINI force-field for the lipid bilayer and the protein. The CG simulation shows chl aggregation in the lipid bilayer which is supported by fluorescence quenching experiments. It is shown that the derived chl model is well suited for CG simulations of stable, structurally consistent, trimeric LHCII and can in the future be used to study their large scale aggregation behavior.
Understanding the influence of dehydration on the membrane structure is crucial to control membra... more Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τα−1, where the α relaxation time (τα) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τα−0.57, showing the signature of glass dynamics. τα and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.
The slow relaxation of interface water (IW) across three primary phases of membranes is relevant ... more The slow relaxation of interface water (IW) across three primary phases of membranes is relevant to understand the influence of IW on membrane functions at supercooled conditions. To this objective, a total of [Formula: see text]s all-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid membranes are carried out. A supercooling-driven drastic slow-down in heterogeneity time scales of the IW is found at the fluid to the ripple to the gel phase transitions of the membranes. At both fluid-to-ripple-to-gel phase transitions, the IW undergoes two dynamic crossovers in Arrhenius behavior with the highest activation energy at the gel phase due to the highest number of hydrogen bonds. Interestingly, the Stokes–Einstein (SE) relation is conserved for the IW near all three phases of the membranes for the time scales derived from the diffusion exponents and the non-Gaussian parameters. However, the SE relation breaks for the time scale obtained from the sel...
All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid memb... more All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes reveal a drastic growth in the heterogeneity length scales of interface water (IW) across fluid to ripple to gel phase transitions. It acts as an alternate probe to capture the ripple size of the membrane and follows an activated dynamical scaling with the relaxation time scale solely within the gel phase. The results quantify the mostly unknown correlations between the spatiotemporal scales of the IW and membranes at various phases under physiological and supercooled conditions.
All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid mem... more All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid membranes reveal a membrane phase transition dictated drastic growth in the interface water (IW) heterogeneity length scales. It acts as an alternate probe to capture the ripple size of the membrane and follows an activated dynamical scaling with the relaxation time scale solely within the gel phase. The results quantify the mostly unknown correlations between the spatio-temporal scales of the IW and membranes at various phases under physiological and supercooled conditions Lipid bilayers form a continuous semipermeable barrier surrounding cells and compartmentalize the intracellular space. They are essential for controlling the dynamics, arrangement, and function of membrane proteins 1 at the fluid (or liquid-crystalline, L α) phase at physiological temperature. The bilayers at the fluid phase comprise of heterogeneous functional microdomains that aid in activities including cell signalling, cell adhesion, and membrane trafficking. Thus, the lateral heterogeneity is accepted as a criterion for the function of a complex biological membrane, specifically in the context of a raft 2 relevant for signalling cascades 3. Quantifying the heterogeneity in a bio-membrane using the current biochemical or biophysical tools is an incredibly challenging task due to the presence of unusual liquid-like domains with microseconds to seconds time scale and nanometers to micrometers length scales having both short and long-range orders. Molecular level characterization of such dynamical domains through experiments is still fragmentary due to the lack of the relevant atomistic trajectories and the unknown spatio-temporal correlations. At physiological temperature interface water molecules (IW) near a single component fluid membrane exhibit signatures of dynamical heterogeneity 4 and can probe regional lipid dynamics which is difficult to access otherwise 5. This is the stepping stone of the current study which aims to measure the spatio-temporal scales of different phases of functionally relevant bilayers through the IW dynamics. Using sum-frequency generation spectroscopy heterogeneity of IW at the watercharged lipid interface has been identified 6. The fluid or disordered membrane undergoes a phase transition to a ripple (P β) phase which quickly changes to a gel (L β) phase 7 upon cooling. The membrane remains in the gel phase upon supercooling. Similar disorder to order transition of the membrane occurs from dehydration induced drastic slowdown in structural relaxation originated from the dynamical heterogeneity of the interface water molecules (IW) 8. Understanding cellular membranes at supercooled temperatures is extremely crucial for cryo-preservation methods, which have a wide range of applications in food science, pharmacology, clinical medicine, and the preservation of human embryos
Biocatalysis is an important area of modern research and is extensively explored by various indus... more Biocatalysis is an important area of modern research and is extensively explored by various industries to attain greener methods in various applications. Supramolecular interactions of short peptides have been under the scanner for developing artificial smart materials inspired from natural systems. Peptide-based artificial enzymes have been proved to show various enzyme-like activities. Therefore, immobilization of catalytic peptides on solid surfaces can be an extremely useful breakthrough for development of cost-effective catalytic formulations. In this work, a series of peptide amphiphiles (PAs) have been systematically analyzed to find the most effective catalyst with esterase like activity. The PA, containing a catalytic triad, 'Asp(Ser)His' in a branched manner, was further immobilized onto silica nanoparticles through covalent bonding method to obtain surface coated catalytic silica nanoparticles. The heterogenous catalytic formulation not only showed enhanced esterase activity than the self-assembled PA in homogenous phase, but also exceeded the activity of natural CV lipase. The catalytic formulation showed high stereoselectivity towards chiral esters. Moreover, the catalyst remained stable at higher temperature, in presence of various denaturant and retained its activity after several catalytic cycles. The ease of separation, robust nature, reusability and high stereoselectivity of the catalyst opens up the possibility of creating new generation heterogeneous catalysts for further industrial applications.
Using path integral approach, we develop variational approximations to the calculation of surviva... more Using path integral approach, we develop variational approximations to the calculation of survival probability for rate processes with dynamical disorder. We derive both upper and lower bounds to the survival probability using Jensen's inequality. The inequalities involve the use of a trial action for which the path integrals can be evaluated exactly. Any parameter in the trial action can be varied to optimize the bounds. We have also derived a lower bound to the rate of the process. As a simple illustration, we apply the method to the problem of a particle undergoing Brownian motion in a harmonic potential well, in the presence of a delta function sink, for which one can calculate the exact survival probability numerically. The calculation confirms the two inequalities. The method should be very useful in similar but more complex problems where even numerical solution is not possible.
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated u... more A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308K to find out the physical sources of universal slow relaxation of hydration layers. Continuously residing interface water (IW) hydrogen bonded to each other and concertedly to different moieties of lipid heads are identified. The non-gaussian parameter of all IW show a crossover from cage vibration to translational diffusion. A significant non-gaussianity is observed for the IW prevailing large length correlations in translational van Hove functions. Two time-scales for the ballisitic motions and hopping transitions are obtained from the self intermediate scattering functions of the IW with an additional long relaxation which disappears for the BW. This is attributed to the coupled dynamics of IW cages hydrogen bonded to lipid heads. Our calculations reveal that the water near membranes are slowed down due to dynamical heterogeneities...
Langmuir : the ACS journal of surfaces and colloids, 2020
The structure and dynamics of interfacial water in biological systems regulate the biochemical re... more The structure and dynamics of interfacial water in biological systems regulate the biochemical reactions. But, it is still enigmatic how the behavior of the interfacial water molecule is controlled. Here, we have investigated the effect of membrane fluidity on the structure and dynamics of interfacial water molecules in biologically relevant phopholipid vesicles. This study delineates that modulation of membrane fluidity through interlipid separation and unsaturation not only mitigate membrane rigidity but also disrupt the strong hydrogen bond (H-bond) network around the lipid bilayer interface. As a result, a disorder in H-bonding between water molecules arises several layers beyond the first hydration shell of the polar headgroup, which essentially modifies the interfacial water structure and dynamics. Furthermore, we have also provided evidence of increasing transportation through these modulated membranes, which enhance the membrane mediated isomerization reaction rate.
Understanding intermolecular interactions among supramolecular self-assembled organization and id... more Understanding intermolecular interactions among supramolecular self-assembled organization and identifying the molecular structure relevant to the self-assembly are crucial for designing materials with desired functionalities. Interactions of aromatic rings in a peptide–perylenediimide conjugate (P-1) are investigated using dispersion-corrected density functional theory. The binding energies of fully optimized dimeric P-1 are calculated to identify the most stable conformation of the dimer. We show that the dispersion correction terms have significant contributions to the total energies of the dimers. The combined results from electronic structure calculations and molecular dynamics simulations demonstrate that the stacked dimer with negative inter-planar angle with clock-wise rotation has stronger binding energy than the dimer with positive inter-planar angle. The excess stability of the dimer with clock-wise rotation is attributed to the intra- and inter-molecular $$\uppi $$ – $$\uppi $$ stacking of the side aromatic rings of the dimer facilitated by formation of less number of hydrogen bonds. The stacked P-1 dimer with negative inter-planar angle and stronger binding energy is identified as the building block of a super structure with left-handed helical arrangements. Our calculations will build the first step towards understanding the molecular origin of the stability of a specific super structure of P-1 over the other, as obtained in the experiment relevant to material science and technology.
The structural basis for the stability of the trimeric form of the light harvesting complex (LHCI... more The structural basis for the stability of the trimeric form of the light harvesting complex (LHCII), a pigmented protein from green plants pivotal for photosynthesis, remains elusive till date. The protein embedded in a dipalmitoylphosphatidylcholine (DPPC) lipid membrane is investigated using all-atom molecular dynamics simulations to find out the interactions responsible for the structural integrity of the trimer and its relation to antenna function. Central association of chlorophyll a (CLA) molecules near the LHCII chains is attributed to a conserved coordination between the Mg of CLA and the oxygen of a specific residue of the first helix of a chain. The residue forms a salt-bridge with the fourth helix of the same chain of the trimer, not of the monomer. In an earlier experiment, three residues (WYR) at each chain of the trimer have been found indispensable for the trimerization and referred to as trimerization motif. We find that the residues of the trimerization motif are connected to the lipids or pigments by a chain of interactions rather than a direct contact. Synergistic effects of sequentially located hydrogen bonds and salt-bridges within monomers of the trimer keep the trimer conformation stable in association with the pigments or the lipids. These interactions are exclusively present in the pigmented trimer and not present in the monomer or in the unpigmented trimer. Thus, our results provide a molecular basis for the inherent stability of the LHCII trimer in a lipid membrane and explain many pre-existing experimental data.
Understanding the influence of dehydration on the membrane structure is crucial to control membra... more Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τα -1, where the α relaxation time (τα) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τα -0.57, showing the signature of glass dynamics. τα and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.
Modulating the structures and properties of biomembranes via permeation of small amphiphilic mole... more Modulating the structures and properties of biomembranes via permeation of small amphiphilic molecules is immensely important, having diverse applications in cell biology, biotechnology, and pharmaceuticals, because their physiochemical and biological interactions lead to new pathways for transdermal drug delivery and administration. In this work, we have elucidated the role of dimethyl sulfoxide (DMSO), broadly used as a penetration-enhancing agent and cryoprotective agent on model lipid membranes, using a combination of fluorescence microscopy and time-resolved fluorescence spectroscopy. Spatially resolved fluorescence lifetime imaging microscopy (FLIM) has been employed to unravel how the fluidity of the DMSO-induced bilayer regulates the structural alteration of the vesicles. Moreover, we have also shown that the dehydration effect of DMSO leads to weakening of the hydrogen bond between lipid headgroups and water molecules and results in faster solvation dynamics as demonstrated by femtosecond time-resolved fluorescence spectroscopy. It has been gleaned that the water dynamics becomes faster because bilayer rigidity decreases in the presence of DMSO, which is also supported by time-resolved rotational anisotropy measurements. The enhanced diffusivity and increased membrane fluidity in the presence of DMSO are further ratified at the single-molecule level through fluorescence correlation spectroscopy (FCS) measurements. Our results indicate that while the presence of DMSO significantly affects the 1,2-dimyristoyl-rac-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-rac-glycero-3-phosphatidylcholine (DPPC) bilayers, it has a weak effect on 1,2-dimyristoyl-sn-glycero-3-phospho-rac-glycerol (DMPG) vesicles, which might explain the preferential interaction of DMSO with the positively charged choline group present in DMPC and DPPC vesicles. The experimental findings have also been further verified with molecular dynamics simulation studies. Moreover, it has been observed that DMSO is likely to have a differential effect on heterogeneous bilayer membranes depending on the structure and composition of their headgroups. Our results illuminate the importance of probing the lipid structure and composition of cellular membranes in determining the effects of cryoprotective agents.
Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the c... more Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a polymer brush. We propose a mesoscopic model for the transport of a protein through the plug, that is general enough to cover both. The protein stretches the plug and creates a local deformation. The bubble so created (prtoein+deformation) executes random walk in the plug. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. Further, on using parameters appropriate for the brush, we find that the diffusion coefficient is much lower. Hence the gel model seems to be more likely explanation for the workings of the plug.
The correct interplay of interactions between protein, pigment and lipid molecules is highly rele... more The correct interplay of interactions between protein, pigment and lipid molecules is highly relevant for our understanding of the association behavior of the light harvesting complex (LHCII) of green plants. To cover the relevant time and length scales in this multicomponent system, a multi-scale simulation ansatz is employed that subsequently uses a classical all atomistic (AA) model to derive a suitable coarse grained (CG) model which can be backmapped into the AA resolution, aiming for a seamless conversion between two scales. Such an approach requires a faithful description of not only the protein and lipid components, but also the interaction functions for the indispensable pigment molecules, chlorophyll b and chlorophyll a (referred to as chl b/chl a). In this paper we develop a CG model for chl b and chl a in a dipalmitoylphosphatidyl choline (DPPC) bilayer system. The structural properties and the distribution behavior of chl within the lipid bilayer in the CG simulations are consistent with those of AA reference simulations. The non-bonded potentials are parameterized such that they fit to the thermodynamics based MARTINI force-field for the lipid bilayer and the protein. The CG simulation shows chl aggregation in the lipid bilayer which is supported by fluorescence quenching experiments. It is shown that the derived chl model is well suited for CG simulations of stable, structurally consistent, trimeric LHCII and can in the future be used to study their large scale aggregation behavior.
Understanding the influence of dehydration on the membrane structure is crucial to control membra... more Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τα−1, where the α relaxation time (τα) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τα−0.57, showing the signature of glass dynamics. τα and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.
The slow relaxation of interface water (IW) across three primary phases of membranes is relevant ... more The slow relaxation of interface water (IW) across three primary phases of membranes is relevant to understand the influence of IW on membrane functions at supercooled conditions. To this objective, a total of [Formula: see text]s all-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid membranes are carried out. A supercooling-driven drastic slow-down in heterogeneity time scales of the IW is found at the fluid to the ripple to the gel phase transitions of the membranes. At both fluid-to-ripple-to-gel phase transitions, the IW undergoes two dynamic crossovers in Arrhenius behavior with the highest activation energy at the gel phase due to the highest number of hydrogen bonds. Interestingly, the Stokes–Einstein (SE) relation is conserved for the IW near all three phases of the membranes for the time scales derived from the diffusion exponents and the non-Gaussian parameters. However, the SE relation breaks for the time scale obtained from the sel...
All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid memb... more All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes reveal a drastic growth in the heterogeneity length scales of interface water (IW) across fluid to ripple to gel phase transitions. It acts as an alternate probe to capture the ripple size of the membrane and follows an activated dynamical scaling with the relaxation time scale solely within the gel phase. The results quantify the mostly unknown correlations between the spatiotemporal scales of the IW and membranes at various phases under physiological and supercooled conditions.
All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid mem... more All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid membranes reveal a membrane phase transition dictated drastic growth in the interface water (IW) heterogeneity length scales. It acts as an alternate probe to capture the ripple size of the membrane and follows an activated dynamical scaling with the relaxation time scale solely within the gel phase. The results quantify the mostly unknown correlations between the spatio-temporal scales of the IW and membranes at various phases under physiological and supercooled conditions Lipid bilayers form a continuous semipermeable barrier surrounding cells and compartmentalize the intracellular space. They are essential for controlling the dynamics, arrangement, and function of membrane proteins 1 at the fluid (or liquid-crystalline, L α) phase at physiological temperature. The bilayers at the fluid phase comprise of heterogeneous functional microdomains that aid in activities including cell signalling, cell adhesion, and membrane trafficking. Thus, the lateral heterogeneity is accepted as a criterion for the function of a complex biological membrane, specifically in the context of a raft 2 relevant for signalling cascades 3. Quantifying the heterogeneity in a bio-membrane using the current biochemical or biophysical tools is an incredibly challenging task due to the presence of unusual liquid-like domains with microseconds to seconds time scale and nanometers to micrometers length scales having both short and long-range orders. Molecular level characterization of such dynamical domains through experiments is still fragmentary due to the lack of the relevant atomistic trajectories and the unknown spatio-temporal correlations. At physiological temperature interface water molecules (IW) near a single component fluid membrane exhibit signatures of dynamical heterogeneity 4 and can probe regional lipid dynamics which is difficult to access otherwise 5. This is the stepping stone of the current study which aims to measure the spatio-temporal scales of different phases of functionally relevant bilayers through the IW dynamics. Using sum-frequency generation spectroscopy heterogeneity of IW at the watercharged lipid interface has been identified 6. The fluid or disordered membrane undergoes a phase transition to a ripple (P β) phase which quickly changes to a gel (L β) phase 7 upon cooling. The membrane remains in the gel phase upon supercooling. Similar disorder to order transition of the membrane occurs from dehydration induced drastic slowdown in structural relaxation originated from the dynamical heterogeneity of the interface water molecules (IW) 8. Understanding cellular membranes at supercooled temperatures is extremely crucial for cryo-preservation methods, which have a wide range of applications in food science, pharmacology, clinical medicine, and the preservation of human embryos
Biocatalysis is an important area of modern research and is extensively explored by various indus... more Biocatalysis is an important area of modern research and is extensively explored by various industries to attain greener methods in various applications. Supramolecular interactions of short peptides have been under the scanner for developing artificial smart materials inspired from natural systems. Peptide-based artificial enzymes have been proved to show various enzyme-like activities. Therefore, immobilization of catalytic peptides on solid surfaces can be an extremely useful breakthrough for development of cost-effective catalytic formulations. In this work, a series of peptide amphiphiles (PAs) have been systematically analyzed to find the most effective catalyst with esterase like activity. The PA, containing a catalytic triad, 'Asp(Ser)His' in a branched manner, was further immobilized onto silica nanoparticles through covalent bonding method to obtain surface coated catalytic silica nanoparticles. The heterogenous catalytic formulation not only showed enhanced esterase activity than the self-assembled PA in homogenous phase, but also exceeded the activity of natural CV lipase. The catalytic formulation showed high stereoselectivity towards chiral esters. Moreover, the catalyst remained stable at higher temperature, in presence of various denaturant and retained its activity after several catalytic cycles. The ease of separation, robust nature, reusability and high stereoselectivity of the catalyst opens up the possibility of creating new generation heterogeneous catalysts for further industrial applications.
Using path integral approach, we develop variational approximations to the calculation of surviva... more Using path integral approach, we develop variational approximations to the calculation of survival probability for rate processes with dynamical disorder. We derive both upper and lower bounds to the survival probability using Jensen's inequality. The inequalities involve the use of a trial action for which the path integrals can be evaluated exactly. Any parameter in the trial action can be varied to optimize the bounds. We have also derived a lower bound to the rate of the process. As a simple illustration, we apply the method to the problem of a particle undergoing Brownian motion in a harmonic potential well, in the presence of a delta function sink, for which one can calculate the exact survival probability numerically. The calculation confirms the two inequalities. The method should be very useful in similar but more complex problems where even numerical solution is not possible.
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated u... more A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308K to find out the physical sources of universal slow relaxation of hydration layers. Continuously residing interface water (IW) hydrogen bonded to each other and concertedly to different moieties of lipid heads are identified. The non-gaussian parameter of all IW show a crossover from cage vibration to translational diffusion. A significant non-gaussianity is observed for the IW prevailing large length correlations in translational van Hove functions. Two time-scales for the ballisitic motions and hopping transitions are obtained from the self intermediate scattering functions of the IW with an additional long relaxation which disappears for the BW. This is attributed to the coupled dynamics of IW cages hydrogen bonded to lipid heads. Our calculations reveal that the water near membranes are slowed down due to dynamical heterogeneities...
Langmuir : the ACS journal of surfaces and colloids, 2020
The structure and dynamics of interfacial water in biological systems regulate the biochemical re... more The structure and dynamics of interfacial water in biological systems regulate the biochemical reactions. But, it is still enigmatic how the behavior of the interfacial water molecule is controlled. Here, we have investigated the effect of membrane fluidity on the structure and dynamics of interfacial water molecules in biologically relevant phopholipid vesicles. This study delineates that modulation of membrane fluidity through interlipid separation and unsaturation not only mitigate membrane rigidity but also disrupt the strong hydrogen bond (H-bond) network around the lipid bilayer interface. As a result, a disorder in H-bonding between water molecules arises several layers beyond the first hydration shell of the polar headgroup, which essentially modifies the interfacial water structure and dynamics. Furthermore, we have also provided evidence of increasing transportation through these modulated membranes, which enhance the membrane mediated isomerization reaction rate.
Understanding intermolecular interactions among supramolecular self-assembled organization and id... more Understanding intermolecular interactions among supramolecular self-assembled organization and identifying the molecular structure relevant to the self-assembly are crucial for designing materials with desired functionalities. Interactions of aromatic rings in a peptide–perylenediimide conjugate (P-1) are investigated using dispersion-corrected density functional theory. The binding energies of fully optimized dimeric P-1 are calculated to identify the most stable conformation of the dimer. We show that the dispersion correction terms have significant contributions to the total energies of the dimers. The combined results from electronic structure calculations and molecular dynamics simulations demonstrate that the stacked dimer with negative inter-planar angle with clock-wise rotation has stronger binding energy than the dimer with positive inter-planar angle. The excess stability of the dimer with clock-wise rotation is attributed to the intra- and inter-molecular $$\uppi $$ – $$\uppi $$ stacking of the side aromatic rings of the dimer facilitated by formation of less number of hydrogen bonds. The stacked P-1 dimer with negative inter-planar angle and stronger binding energy is identified as the building block of a super structure with left-handed helical arrangements. Our calculations will build the first step towards understanding the molecular origin of the stability of a specific super structure of P-1 over the other, as obtained in the experiment relevant to material science and technology.
The structural basis for the stability of the trimeric form of the light harvesting complex (LHCI... more The structural basis for the stability of the trimeric form of the light harvesting complex (LHCII), a pigmented protein from green plants pivotal for photosynthesis, remains elusive till date. The protein embedded in a dipalmitoylphosphatidylcholine (DPPC) lipid membrane is investigated using all-atom molecular dynamics simulations to find out the interactions responsible for the structural integrity of the trimer and its relation to antenna function. Central association of chlorophyll a (CLA) molecules near the LHCII chains is attributed to a conserved coordination between the Mg of CLA and the oxygen of a specific residue of the first helix of a chain. The residue forms a salt-bridge with the fourth helix of the same chain of the trimer, not of the monomer. In an earlier experiment, three residues (WYR) at each chain of the trimer have been found indispensable for the trimerization and referred to as trimerization motif. We find that the residues of the trimerization motif are connected to the lipids or pigments by a chain of interactions rather than a direct contact. Synergistic effects of sequentially located hydrogen bonds and salt-bridges within monomers of the trimer keep the trimer conformation stable in association with the pigments or the lipids. These interactions are exclusively present in the pigmented trimer and not present in the monomer or in the unpigmented trimer. Thus, our results provide a molecular basis for the inherent stability of the LHCII trimer in a lipid membrane and explain many pre-existing experimental data.
Understanding the influence of dehydration on the membrane structure is crucial to control membra... more Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τα -1, where the α relaxation time (τα) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τα -0.57, showing the signature of glass dynamics. τα and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.
Uploads
Papers by Ananya Debnath