Niraj Modi

Publications (5) View all

• Article: Modeling the Ion Selectivity of the Phosphate Specific Channel OprP

  Niraj Modi,, Roland Benz ,, Robert E. W. Hancock,, Ulrich Kleinekathöfer
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  ABSTRACT: Ion selectivity of transport systems is an essential property of membranes from living organisms. These entities are used to regulate multifarious biological processes by virtue of selective participation of specific ions in transport processes. To understand this process, we studied the phosphate selectivity of the OprP porin from Pseudomonas aeruginosa using all-atom free-energy molecular dynamics simulations. These calculations were performed to define the energetics of phosphate, sulfate, chloride, and potassium ion transport through OprP. Atomic-level analysis revealed that the overall electrostatic environment of the channel was responsible for the anion selectivity of the channel, whereas the particular balance of interactions between the permeating ions and water as well as channel residues drove the selectivity between different anions. The selectivity of OprP is discussed in light of well-studied ion channels that are highly selective for potassium or chloride.
  Journal of Physical Chemistry Letters 11/2012; 3(23):3639-3645. · 6.21 Impact Factor
• Article: Pulling Peptides across Nano-Channels: Resolving Peptide Binding and Translocation through The Hetero-Oligomeric Channel from Nocardia farcinica.

  Pratik Raj Singh, Ivan Bárcena-Uribarri, Niraj Modi, Ulrich Kleinekathoefer, Roland Benz, Mathias Winterhalter, Kozhinjampara R Mahendran
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  ABSTRACT: We investigated translocation of cationic peptides through nano-channels derived from the Gram positive bacterium Nocardia farcinica at the single molecule level. The two subunits NfpA and NfpB form a hetero-oligomeric cation selective channel. Based on amino acid comparison we performed homology modeling and obtained a channel structurally related to MspA of Mycobacterium smegmatis. The quantitative single-molecule measurements provide an insight into transport processes of solutes through nano-channels. High resolution ion conductance measurements in the presence of peptides of different charge and length revealed the kinetics of peptide binding. The observed asymmetry in peptide binding kinetics indicated a unidirectional channel insertion in lipid bilayer. In the case of cationic peptides, the external voltage acts as a driving force that promotes the interaction of the peptide with the channel surface. At low voltage, the peptide just binds to the channel whereas at higher voltage, the force is strong enough to pull the peptide across the channel. This allows distinguishing quantitatively between peptide binding and translocation through the channel.
  ACS Nano 11/2012; · 10.77 Impact Factor
• Article: Computational modeling of ion transport through nanopores.

  Niraj Modi, Mathias Winterhalter, Ulrich Kleinekathöfer
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  ABSTRACT: Nanoscale pores are ubiquitous in biological systems while artificial nanopores are being fabricated for an increasing number of applications. Biological pores are responsible for the transport of various ions and substrates between the different compartments of biological systems separated by membranes while artificial pores are aimed at emulating such transport properties. As an experimental method, electrophysiology has proven to be an important nano-analytical tool for the study of substrate transport through nanopores utilizing ion current measurements as a probe for the detection. Independent of the pore type, i.e., biological or synthetic, and objective of the study, i.e., to model cellular processes of ion transport or electrophysiological experiments, it has become increasingly important to understand the dynamics of ions in nanoscale confinements. To this end, numerical simulations have established themselves as an indispensable tool to decipher ion transport processes through biological as well as artificial nanopores. This article provides an overview of different theoretical and computational methods to study ion transport in general and to calculate ion conductance in particular. Potential new improvements in the existing methods and their applications are highlighted wherever applicable. Moreover, representative examples are given describing the ion transport through biological and synthetic nanopores as well as the high selectivity of ion channels. Special emphasis is placed on the usage of molecular dynamics simulations which already have demonstrated their potential to unravel ion transport properties at an atomic level.
  Nanoscale 10/2012; 4(20):6166-80. · 5.91 Impact Factor
• Article: Probing the Transport of Ionic Liquids in Aqueous Solution through Nanopores

  Niraj Modi, Pratik Raj Singh, Kozhinjampara R. Mahendran, Robert Schulz, Mathias Winterhalter, Ulrich Kleinekathöfer
  Journal of Physical Chemistry Letters 08/2011; 2(18):2331-2336. · 6.21 Impact Factor
• Source

  Available from: Nilanjan Roy

  Article: Probing the binding site of curcumin in Escherichia coli and Bacillus subtilis FtsZ--a structural insight to unveil antibacterial activity of curcumin.

  Simranjeet Kaur, Niraj H Modi, Dulal Panda, Nilanjan Roy
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  ABSTRACT: The cytoskeletal protein, FtsZ plays a pivotal role in prokaryotic cell division and is present in majority of the bacterial species. In recent years, inhibitors of FtsZ have been identified that may function as lead compounds for the development of novel antimicrobials. It has been found that curcumin, the main bioactive component of Curcuma longa, inhibits Bacillus subtilis and Escherichia coli growth by inhibiting FtsZ assembly. Though it is experimentally established that curcumin inhibits FtsZ polymerization, the binding site of curcumin in FtsZ is not known. In this study, interaction of curcumin with catalytic core domain of E. coli and B. subtilis FtsZ was investigated using computational docking.
  European journal of medicinal chemistry 09/2010; 45(9):4209-14. · 3.27 Impact Factor