Thematic Unit of Excellence on Computational Materials Science

Salt Lake, India

Thematic Unit of Excellence on Computational Materials Science

Salt Lake, India

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Saha P.,se National Center For Basic Science | Sikdar S.,se National Center For Basic Science | Manna C.,se National Center For Basic Science | Chakrabarti J.,se National Center For Basic Science | And 2 more authors.
RSC Advances | Year: 2017

STY3178 is a yfdX protein from Salmonella Typhi. yfdX proteins occur ubiquitously in a number of virulent bacteria but their cellular localization is unknown. Our earlier studies have shown that STY3178 is a trimer and can be a periplasmic chaperone protein. In the present study we show the stability of STY3178 in the presence of the bio-mimetic anionic surfactant sodium dodecyl sulphate (SDS). With increasing concentrations of SDS we observe monomeric STY3178 which reversibly forms the trimer upon decreasing the surfactant concentration. Protein tertiary structure is not perturbed in the presence of SDS. We show using molecular dynamics simulation and conformational thermodynamics data that SDS induces stability of the monomer compared to an isolated monomer of STY3178. This supports our experimental observations. © 2017 The Royal Society of Chemistry.


Tyagi C.,Jawaharlal Nehru University | Bathke J.,Justus Liebig University | Goyal S.,Banasthali University | Fischer M.,Justus Liebig University | And 4 more authors.
International Journal of Biochemistry and Cell Biology | Year: 2015

Glutathione reductase (GR), a homodimeric FAD-dependent disulfide reductase, is essential for redox homeostasis of the malaria parasite Plasmodium falciparum and has been proposed as an antimalarial drug target. In this study we performed a virtual screening against PfGR, using the structures of about 170,000 natural compounds. Analysis of the two top-scoring molecules, TTB and EPB, indicated that these ligands are likely to interact with the homodimer intersubunit cavity of PfGR with high binding energy scores of -9.67 and -9.60 kcal/mol, respectively. Both compounds had a lower affinity for human GR due to differences in structure and electrostatic properties. In order to assess the putative interactions in motion, molecular dynamics simulations were carried out for 30 ns, resulting in TTB being more dynamically and structurally favored than EPB. A closely related compound MDPI 21618 was tested on recombinant PfGR and hGR, resulting in IC50 values of 11.3 ± 2.5 μM and 10.2 ± 1.7 μM, respectively. Kinetic characterization of MDPI 21618 on PfGR revealed a mixed-type inhibition with respect to glutathione disulfide (Ki = 9.7 ± 2.3 μM) and an uncompetitive inhibition with respect to NADPH. Furthermore, MDPI 21618 was found to inhibit the growth of the chloroquine-sensitive P. falciparum strain 3D7 with an IC50 of 3.2 ± 1.9 μM and the chloroquine-resistant Dd2 strain with an IC50 of 3.2 + 1.6 μM. In drug combination assays with chloroquine, artemisinin, or mefloquine MDPI 21618 showed an antagonistic action, which might suggest partially overlapping routes of action. This study further substantiates research on PfGR as a potential antimalarial drug target. © 2015 Elsevier Ltd. All rights reserved.


PubMed | Jawaharlal Nehru University, Leibniz Institute for Natural Product Research and Infection Biology, Justus Liebig University, Banasthali University and Thematic Unit of Excellence on Computational Materials Science
Type: | Journal: The international journal of biochemistry & cell biology | Year: 2015

Glutathione reductase (GR), a homodimeric FAD-dependent disulfide reductase, is essential for redox homeostasis of the malaria parasite Plasmodium falciparum and has been proposed as an antimalarial drug target. In this study we performed a virtual screening against PfGR, using the structures of about 170,000 natural compounds. Analysis of the two top-scoring molecules, TTB and EPB, indicated that these ligands are likely to interact with the homodimer intersubunit cavity of PfGR with high binding energy scores of -9.67 and -9.60kcal/mol, respectively. Both compounds had a lower affinity for human GR due to differences in structure and electrostatic properties. In order to assess the putative interactions in motion, molecular dynamics simulations were carried out for 30ns, resulting in TTB being more dynamically and structurally favored than EPB. A closely related compound MDPI 21618 was tested on recombinant PfGR and hGR, resulting in IC50 values of 11.32.5M and 10.21.7M, respectively. Kinetic characterization of MDPI 21618 on PfGR revealed a mixed-type inhibition with respect to glutathione disulfide (Ki=9.72.3M) and an uncompetitive inhibition with respect to NADPH. Furthermore, MDPI 21618 was found to inhibit the growth of the chloroquine-sensitive P. falciparum strain 3D7 with an IC50 of 3.21.9M and the chloroquine-resistant Dd2 strain with an IC50 of 3.2+1.6M. In drug combination assays with chloroquine, artemisinin, or mefloquine MDPI 21618 showed an antagonistic action, which might suggest partially overlapping routes of action. This study further substantiates research on PfGR as a potential antimalarial drug target.


Sikdar S.,Sn Bose National Center For Basic Science | Chakrabarti J.,Sn Bose National Center For Basic Science | Chakrabarti J.,Thematic Unit of Excellence on Computational Materials Science | Ghosh M.,Sn Bose National Center For Basic Science
Molecular BioSystems | Year: 2014

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-galactosyltransferase (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. © the Partner Organisations 2014.


Das A.,Sn Bose National Center For Basic Science | Chakrabarti J.,Sn Bose National Center For Basic Science | Chakrabarti J.,Thematic Unit of Excellence on Computational Materials Science | Ghosh M.,Sn Bose National Center For Basic Science
Chemical Physics Letters | Year: 2013

Conformational changes in proteins induced by metal-ions play extremely important role in various cellular processes and technological applications. Dihedral angles are suitable conformational variables to describe microscopic conformations of a biomacromolecule. Here, we use the histograms of the dihedral angles to study the thermodynamics of conformational changes of a protein upon metal-ion binding. Our method applied to Ca2+ ion binding to an important metalloprotein, Calmodulin, reveals different thermodynamic changes in different metal-binding sites. The ligands coordinating to Ca2+ ions also play different roles in stabilizing the metal-ion coordinated protein-structure. Metal-ion binding induce remarkable thermodynamic changes in distant part of the protein via modification of secondary structural elements. © 2013 Elsevier B.V. All rights reserved.


Das A.,Sn Bose National Center For Basic Science | Ghosh M.,Sn Bose National Center For Basic Science | Chakrabarti J.,Sn Bose National Center For Basic Science | Chakrabarti J.,Thematic Unit of Excellence on Computational Materials Science
Chemical Physics Letters | Year: 2016

We calculate the time dependent correlation functions (TDCF) between the dihedral angles of a protein calmodulin (CaM), an important protein involved in calcium ion binding in eukaryotic cells. The linker between the calcium binding domains of CaM shows structural changes due to calcium binding at far distances which enables the protein to function. We show that the TDCF between the dihedral angles in these regions are correlated temporally prior to ion binding which are lost upon ion binding. Thus the TDCFs connect the structural changes with ion binding, and can be useful to understand coupled phenomena in bio-macromolecules. © 2016 Elsevier B.V.All rights reserved.


Saha P.,se National Center For Basic Science | Sikdar S.,se National Center For Basic Science | Chakrabarti J.,se National Center For Basic Science | Chakrabarti J.,Thematic Unit of Excellence on Computational Materials Science | Ghosh M.,se National Center For Basic Science
RSC Advances | Year: 2016

yfdX proteins occur in a large number of virulent bacteria. Recently we have shown that STY3178, a yfdX protein from Salmonella Typhi, exists in a trimeric state in solution which is capable of interacting with antibiotics, stable at elevated temperatures and undergoes reversible thermal unfolding. In this present study, we report the chemical response of STY3178. We monitor the stability of the protein in presence of chaotropes. It can regain the native-like structure from the chaotrope induced unfolded states. The structural stability of this protein is further studied in a wide pH range which reveals that the STY3178 trimer is stable in both acidic as well as basic media. We further show that the protein interacts with oxalate in vitro. Finally, we perform computational studies viz. modeling and molecular dynamics simulation to understand the stability of trimeric STY3178 over its monomer conformation. The conformational thermodynamic changes indicate that oligomerization induces stability via salt bridge interactions, present at the monomer interface. © 2016 The Royal Society of Chemistry.


Chacko S.,Thematic Unit of Excellence on Computational Materials Science | Nafday D.,se National Center For Basic Science | Kanhere D.G.,University of Pune | Saha-Dasgupta T.,Thematic Unit of Excellence on Computational Materials Science
Physical Review B - Condensed Matter and Materials Physics | Year: 2014

We investigate the many-body-instability-driven electronic, magnetic, and thermodynamic properties of graphene nanoflakes described by an extended Hubbard model using exact diagonalization. Our exact results lead to a complete magnetic phase diagram in n-V space, where n is the filling and V is the nonlocal Coulomb interaction. The phase diagram is found to consist of reentrant phases with net magnetic moment, separated by those with zero magnetic moment. The interplay of local and nonlocal Coulomb interaction, geometry, and filling gives rise to complex magnetic phases with coexisting antiferromagnetic and ferromagnetic correlations, of both short-range and long-range nature. A small change in temperature or in the strength of the nonlocal Coulomb interaction is found to drive the change in the magnetic state. The low-temperature thermodynamic behavior, driven by the crossover of eigenstates of contrasting magnetic characters, is signaled by a sharp peak in the specific heat. © 2014 American Physical Society.


Das A.,se National Center For Basic Science | Chakrabarti J.,se National Center For Basic Science | Chakrabarti J.,Thematic Unit of Excellence on Computational Materials Science | Ghosh M.,se National Center For Basic Science
Molecular BioSystems | Year: 2014

Recent experiments with biomacromolecular complexes suggest that structural modifications at the interfaces are vital for stability of the complexes and the functions of the biomacromolecules. Although several qualitative aspects about such interfaces are known from structural data, quantification of the interfacial changes is lacking. In this work, we study the thermodynamic changes at the interface in the complex between an enzyme, Nuclease A (NucA), and a specific inhibitor protein, NuiA. We calculate the conformational free energy and conformational entropy costs from histograms of the dihedral angles generated from all-atom molecular dynamics simulations on the complex and the free proteins. We extract the conformational thermodynamic parameters for changes in the tertiary structure of NuiA. We show that the binding is dominated by the interfacial changes, where the basic residues of NucA and acidic residues of NuiA are highly ordered and stabilized via strong electrostatic interactions. Our results correlate well with known information from structural studies. The tight interfacial structure is reflected in the significant changes in the structure and dynamics of the water molecules at the enzyme-inhibitor interface. The interfacial water molecules contribute significantly to the entropy loss for the overall complexation. © 2014 The Royal Society of Chemistry.


Moitra A.,Thematic Unit of Excellence on Computational Materials Science
Computational Materials Science | Year: 2013

The strength of nanocrystalline (NC) hexagonal closed packed (hcp) magnesium has been studied using computer simulations. Three dimensional NC magnesium materials are developed using Voronoi tessellation in which a random distribution of grains is generated. The microstructural properties and mechanical behaviors under tensile loading are investigated using molecular dynamics simulations. A size scale effect related to the yield stress in the specimen is evidenced. A transition from grain size softening to grain size hardening has been observed for a 10 nm average grain size. © 2013 Elsevier B.V. All rights reserved.

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