Studies on Bio-macro molecular complexes:

Researches related to bio-molecular systems:

We perform detailed computation and theoretical analysis on conformational changes in bio macro molecular complexes, like, protein-metal ion, protein-protein, protein-ligand structures which forms the heart of all bio chemical activities. These activities may be broadly classified as follows.

A. Microscopic studies: 

1.     Insight on protein functions:

          We have developed a method for calculating the thermodynamics of conformational changes in bio-molecular complexes     based on the distribution of the dihedral angles. We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically (Click Here For Details).

          Based on this we seek microscopic view of protein functions. 

          We show that the thermodynamics of metal ion-induced conformational changes aid to understand the functions of protein complexes. This is illustrated in the case of a metalloprotein, alpha-lactalbumin (aLA), a divalent metal ion binding protein. We use the histograms of dihedral angles of the protein, generated from all-atom molecular dynamics simulations, to calculate conformational thermodynamics. The thermodynamically destabilized and disordered residues in different conformational states of a protein are proposed to serve as binding sites for ligands. This is tested for β-1,4 galactosyltransf- erase (β4GalT) binding to the Ca2+–aLA complex, in which the binding residues are known. Among the binding residues, the C-terminal residues like aspartate (D) 116, glutamine (Q) 117, tryptophan (W) 118 and leucine (L) 119 are destabilized and disordered and can dock β4GalT onto Ca2+–aLA. No such thermodynamically favourable binding residues can be identified in the case of the Mg2+–aLA complex. We apply similar analysis to oleic acid binding and predict that the Ca2+–aLA complex can bind to oleic acid through the basic histidine (H) 32 of the A2 helix and the hydrophobic residues, namely, isoleucine (I) 59, W60 and I95, of the interfacial cleft. However, the number of destabilized and disordered residues in Mg2+–aLA are few, and hence, the oleic acid binding to Mg2+-bound aLA is less stable than that to the Ca2+–aLA complex. Our analysis can be generalized to understand the functionality of other ligand bound proteins (Click Here For Details)

         Currently we are trying to understand protein-DNA interactions and therapeutical protein complexes using stability of conformational changes.

2.     Dynamic aspects of conformational fluctuations:  

           The microscopic basis of communication among the functional sites in bio-macromolecules is a fundamental challenge in uncovering their functions. We study the communication through temporal cross-correlation among the binding sites. We illustrate via Molecular Dynamics simulations the properties of the temporal cross-correlation between the dihedrals of a small protein, ubiquitin which participates in protein degradation in eukaryotes. We show that the dihedral angles of the residues possess non-trivial temporal cross-correlations, having peaks at low frequencies with time scales in nano-seconds and an algebraic tail with a universal exponent for large frequencies. We show the existence of path for temporally correlated degrees of freedom among the functional residues. We explain the qualitative features of the cross-correlations through a general mathematical model. The generality of our analysis suggests that temporal cross-correlation functions may provide convenient theoretical framework to understand bio-molecular functions on microscopic basis (Click Here For Details).

            Currently we are trying to find correlation between dihedral fluctuations  and bond fluctuations of ubiquitin protein from the simulated trajectories. Dihedral fluctuations are not directly amenable  to experimental measurements, whereas bond vector fluctuation can be measured experimentally using the  Nuclear Magnetic Resonance technique. Our work may provide a route to verify experimentally the theoretical results using dihedral fluctuation. 

3.     Quantum Mechanical effects: 

The coordination of metal ions to a protein leads to substantial electronic redistribution which governs the stability of metallo-proteins. This leads us to undertake ab-initio calculations for metal binding regions, using density functional theory.

Quantum chemical (QC) calculations for macromolecules require truncation of the molecule, highlighting the portion of interest due to heavy computation cost. As a result, an estimation of the effects of truncation is important to interpret the energy spectrum of such calculations. We perform density functional theory based QC calculations on calcium ion bound EF-hand loops of Calmodulin isolated from the crystal structure in an implicit solvent. We find that the terminal contributions of neutral capping are negligible across the entire ground-state energy spectrum. The coordination energy range and the nature of hybridization of the coordination state molecular orbitals remain qualitatively similar across these loops. While the HOMO and LUMO of loops in the N-terminal domain are dominated by the acidic aspartates, and the polar/hydrophobic residues, respectively, these levels of the C-terminal domain loops show strong localized electron density on the phenyl rings of the tyrosines. The Fukui index calculation identifies the hydroxyl oxygen in the phenyl ring of Y99 as a potent nucleophile. Our analysis indicates a general way of interpreting the electronic energy spectra to understand stability and functions of large biomolecules where the truncation of the molecule and, hence, the terminal capping effects are inevitable (Click Here For Details).

Currently we are working on the interaction between metal oxide surfaces and bio molecules which have applications in biomedical and nano technological areas. Among others, zinc oxide, titanium oxide etc are the most considered for this kind of interfaces. A fundamental understanding on the adhesion mechanism of these bio molecules on metal oxide surfaces is still elusive. Here our aim is to study the interactions of different bio molecules with ZnO surfaces using the density functional theory. 

B. Modeling large scale behavior of bio-macro molecular systems:

          The large scale behaviour of bio-molecular systems can not be achieved by full atomistic calculations. Self-assembly of proteins is one such area. Self-assembly at nano-meter length scale by amphiphilic molecules are relevant not only in several neuro degenerative disorders but also in nano-bio technology.  We study protein aggregation using a model system of particles having charge at the core but with solvent repelling surface using Monte-Carlo (MC) simulations and mean field analytical treatment. We observe from our simulations that the hydrophobic particles with mutual harmonic interaction of strength α , exhibit aggregation. Electrostatic repulsion between the particles characterized by Debye screening length 1/κ , controls stability of finite clusters or aggregates, the threshold of aggregation being  α  ∽ κ ^(-1.5). We support our observations qualitatively from mean field analysis.

We are interested to study the kinetics of cluster formation of this model system.

 Equilibrium and non-equilibrium studies on colloidal systems:

Colloidal systems represent a model soft matter system which can be used to study the condensed matter properties both in equilibrium and out of equilibrium. We have made attempts to understand dynamics of colloidal systems driven by electric field.

In a model system of oppositely charged colloids we study via Brownian dynamics simulation the dynamical response as the system approaches steady states upon application of a constant electric field. The system is known to form patterns of like charges in the transverse plane to the field that are elongated along the field as lanes. We  increase in structural heterogeneity leads to non-Gaussian tails in the probability distribution of particle displacements [self van Hove functions (self-vHfs)]. The self-diffusion coefficient depends upon the time of the observations and consequently indicates aging in the system. However, the anomalies in the self-vHfs and diffusion do not appear during the melting of the structures (Click Here For Details).

The interplay between structure and dynamics in non-equilibrium steady-state is far from understood. We address this issue by tracking Brownian Dynamics trajectories of particles in lane forming colloids. The particles show crossover from homogeneous to lane state, a prototype of heterogeneous structure formation in non-equilibrium systems. We show that the length scale of structural correlations controls heterogeneity in diffusion and consequent anomalous dynamic responses, like the exponential tail in the probability distributions of particle displacements and stretched exponential structural relaxation. We generalise our observations using equations for steady-state density which may help to understand the microscopic basis of heterogeneous diffusion in condensed matter systems (Click Here For Details).

We are carrying out studies on dynamics of colloids in variety of non-equilibrium conditions.