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H H, Mallajosyula SS. Unveiling DNA Translocation in Pristine Graphene Nanopores: Understanding Pore Clogging via Polarizable Simulations. ACS Appl Mater Interfaces 2023; 15:55095-55108. [PMID: 37965826 DOI: 10.1021/acsami.3c12262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Graphene has garnered remarkable attention in recent years as an attractive nanopore membrane for rapid and accurate sequencing of DNA. The inherent characteristics of graphene offer exquisite experimental control over pore dimensions, encompassing both the width (pore diameter) and height. Despite these promising prospects, the practical deployment of pristine graphene nanopores for DNA sequencing has encountered a formidable challenge in the form of pore clogging, which is primarily attributed to hydrophobic interactions. However, a comprehensive understanding of the atomistic origins underpinning this clogging phenomenon and the nuanced impact of individual nucleobase identities on clogging dynamics remain an underexplored domain. Elucidating the atomistic intricacies governing pore clogging is pivotal to devising strategies for its mitigation and advancing our understanding of graphene nanopore behavior. We harness Drude polarizable simulations to systematically dissect the nucleobase-dependent mechanisms that play a pivotal role in nanopore clogging. We unveil nucleobase-specific interactions that illuminate the multifaceted roles played by both hydrophobic and electrostatic forces in driving nanopore clogging events. Notably, the Drude simulations also unveil the bias-dependent translocation dynamics and its pivotal role in alleviating pore clogging─a facet that remains significantly underestimated in conventional additive (nonpolarizable) simulations. Our findings underscore the indispensability of incorporating polarizability to faithfully capture the intricate dynamics governing graphene nanopore translocation phenomena, thus deepening our insights into this crucial field.
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Affiliation(s)
- Hemanth H
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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H H, Mewada R, Mallajosyula SS. Capturing charge and size effects of ions at the graphene-electrolyte interface using polarizable force field simulations. Nanoscale Adv 2023; 5:796-804. [PMID: 36756506 PMCID: PMC9891073 DOI: 10.1039/d2na00733a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/27/2022] [Indexed: 06/18/2023]
Abstract
We present a systematic investigation capturing the charge and size effects of ions interacting with a graphene surface using polarizable simulations. Our results utilizing the Drude polarizable force field (FF) for ions, water and graphene surfaces, show that the graphene parameters previously developed by us are able to accurately capture the dynamics at the electrolyte-graphene interface. For monovalent ions, with increasing size, the solvation shell plays a crucial role in controlling the ion-graphene interactions. Smaller monovalent ions directly interact with the graphene surface, while larger ions interact with the graphene surface via a well-formed solvation shell. For divalent ions, both interaction modes are observed. For the anion Cl-, we observe direct interaction between the ions and the graphene surface. The anion-graphene interactions are strongly driven by the polarizability of the graphene surface. These effects are not captured in the absence of polarization by additive FF simulations. The present study underlines the importance of polarizability in capturing the interfacial phenomenon at the solid-solute interface.
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Affiliation(s)
- Hemanth H
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar Palaj Gujarat India-382355
| | - Rohan Mewada
- Discipline of Material Science and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat India-382355
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar Palaj Gujarat India-382355
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3
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Abstract
Analysis of crystal structures of hexose monosaccharides α-d-mannose (α-MAN), β-d-mannose (β-MAN), α-d-glucose (α-GLC), β-d-glucose (β-GLC), α-d-galactose (α-GAL), β-d-galactose (β-GAL), α-d-altrose (α-ALT), β-d-altrose (β-ALT), α-d-idose (α-IDO), and β-d-idose (β-IDO) reveals that the monosaccharide ring adopts multiple ring conformations. These ring conformations can be broadly classified as chair, half-chair, envelope, boat, and skew-boat conformations. The ability of the monosaccharide ring to adopt multiple conformations has been closely tied with their bioactivity. However, it has been difficult to capture the dynamic information of these conformations from experimental studies. Even from simulations, capturing these different conformations is challenging because of the energy barriers involved in the transitions between the stable 4C1 and 1C4 chair forms. In this study, we analyze the influence of the polarizable force field on the ring dynamics of five major types of unsubstituted aldohexoses─glucose, mannose, galactose, altrose, and idose─and their anomers. We simulate microsecond trajectories to capture the influence of the CHARMM36 additive and polarizable carbohydrate force fields on the ring dynamics. The microsecond trajectories allow us to comment on the issues associated with equilibrium molecular dynamics simulations. Further, we use the extended system adaptive biasing force (eABF) method to compare the conformational sampling efficiencies of the additive and polarizable force fields. Our studies reveal that inclusion of polarization enhances the sampling of ring conformations and lowers the energy barriers between the 4C1 and 1C4 conformations. Overall, the CHARMM36 additive force field is observed to be rigid and favor the 4C1 conformations. Although the inclusion of polarizability results in enhancing ring flexibility, we observe sampling that does not agree with experimental results, warranting a revision of the polarizable Drude parameters.
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Affiliation(s)
- Chythra J N
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat382355, India
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat382355, India
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Rani L, Arora A, Majhi S, Mishra A, Mallajosyula SS. Experimental and simulation studies reveal mechanism of action of human defensin derivatives. Biochim Biophys Acta Biomembr 2022; 1864:183824. [PMID: 34838874 DOI: 10.1016/j.bbamem.2021.183824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial peptides (AMPs) are naturally occurring promising candidates which can be used as antibiotics against a wide variety of bacteria. The key component for using them as a potent antibiotic is that their mechanism of action is less prone to bacterial resistance. However, the molecular details of their mechanism of action is not yet fully understood. In this study, we try to shed light on the mode of action of AMPs, possible reason behind it, and their interaction with lipid bilayers through experimental as well as molecular dynamics (MD) simulation studies. The focal of our study was Human beta defensin 3 (hBD-3) which is a naturally occurring AMP. We chose three derivatives of hBD-3, namely CHRG01, KSR, and KLR for the detailed analysis presented in this study. These three peptides are evaluated for their antibacterial potency, secondary structure analysis and mechanism of action. The experimental results reveal that these peptides are active against gram positive as well as gram negative bacteria and kill bacteria by forming membrane pores. The MD simulation results correlate well with the antibacterial activity and shed light into the early membrane insertion dynamics. Moreover, the specific amino acids responsible for membrane disruptions are also identified from the MD simulations. Understanding the molecular level interaction of individual amino acids with the lipid bilayer will greatly help in the design of more efficient antimicrobial peptides.
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Affiliation(s)
- Lata Rani
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Ankita Arora
- Department of Materials Science and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Sasmita Majhi
- Department of Materials Science and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Abhijit Mishra
- Department of Materials Science and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India.
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India.
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Rani L, Mallajosyula SS. Site-Specific Stabilization and Destabilization of α Helical Peptides upon Phosphorylation and O-GlcNAcylation. J Phys Chem B 2021; 125:13444-13459. [PMID: 34870441 DOI: 10.1021/acs.jpcb.1c09419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Helices (α-helix) are the most common type of secondary structure motif present in proteins. In this study, we have investigated the structural influence of phosphorylation and O-GlcNAcylation, common intracellular post-translational modifications (PTMs), on the α-helical conformation. The simulation studies were performed on the Baldwin model α-helical peptide sequence (Ac-AKAAAAKAAAAKAA-NH2). The Baldwin sequences were chosen due to the availability of site-specific experimental post-translational data for cross-validation with the simulations. The influence of PTMs was examined across the span of the α-helix, namely, at the N-terminus, position 10 (interior region), and the C-terminus for both serine and threonine residues placed at these positions. Molecular dynamics (MD) simulations revealed that phosphorylation and O-GlcNAcylation at the N-terminus lead to the stabilization of the helical conformation. PTMs in the interior or the C-terminus were found to disrupt helicity, with the disruption being more pronounced for PTMs in the interior region, in accordance with experimental studies. It was found that phosphorylation-derived destabilization was mainly due to the formation of an intraresidue HN-PO32- electrostatic interaction and interactions between the phosphate group and the side chain of adjacent lysine residues (NH3···PO32-). Hydrophobic and steric clashes were the main causes of destabilization in the case of O-GlcNAcylation. The structural disruptions were found to be more pronounced for PTM at the threonine site when compared to the serine site. The salt-bridge-dependent stability of the α-helix was found to be highly position specific, an i → i + 4 interaction stabilizing the helix, with other placements leading to the destabilization of the helix.
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Affiliation(s)
- Lata Rani
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, Gujarat, India
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, Gujarat, India
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Abstract
Taupathies involve the deposition of abnormal tau protein into neurofibrillary tangles (NFTs) in the human brain. The abnormally hyperphosphorylated tau dissociates from microtubules and forms insoluble aggregates known as paired helical filaments (PHFs), highlighting the importance of post-translational modifications in taupathies. The present study examines the factors responsible for the structural stability of PHFs in native as well as in phosphorylated and O-GlcNAcylated tau. We carried out molecular dynamics simulations on the R3-R4 repeat domains of the human tau protein to gain atomic insights into the key noncovalent interactions responsible for their unique dimeric C-shaped structure. The structural effects upon post-translational modification were found to be prominent for phosphorylation when compared with O-GlcNAcylation. O-GlcNAcylated tau was found to retain the "C conformation" observed in the native tau PHF, whereas upon phosphorylation, we observed a conformational transition to a more opened "H conformation". We found that this conformational transition is brought about by the loss of a key salt bridge between Lys353 and Asp358 due to the phosphorylation at Ser356 that results in the reorganization of the dimeric interface.
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Affiliation(s)
- Lata Rani
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, Gujarat, India
| | - Sairam S. Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, Gujarat, India
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Abstract
In recent years, graphene has attracted attention from researchers as an atomistically thin solid state material for the study on the self-assembly of nucleobases. Non-covalent interactions between nucleobases and graphene sheets play a fundamental role in understanding the self-assembly of nucleobases on the graphene sheet. A fundamental understanding of the effect of molecular polarizability on these non-covalent interactions between the nucleobases and the underlying graphene sheet is absent in the literature. In this paper, we present the results from polarizable molecular dynamics simulation studies to understand the effect of polarization on the strength of non-covalent interactions. To this end, we report the development of Drude parameters for describing the polarizable graphene sheet. The developed parameters were used to study the self-aggregation phenomenon of nucleobases on a graphene support. We observe a significant change in the interaction patterns upon the inclusion of polarization into the system, with polarizable simulations yielding results that closely resemble the experimental studies. Two of the key observations were the probability of the formation of stacks in guanine-rich systems, and the spontaneous formation of H-bonded structures over the graphene sheet, which allude to the importance of the DNA sequence and composition. Both these effects were not observed in the additive simulations. The present study sheds light on the effect of polarization on the adsorption of DNA nucleobases on a graphene sheet, but the methodology can be extended to include a variety of small molecules and complete DNA strands.
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Affiliation(s)
- Hemanth H
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India-382355.
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India-382355.
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Abstract
The microtubule-associated protein Tau (MAPT) is a phosphoprotein in neurons of the brain. Aggregation of Tau is the leading cause of tauopathies such as Alzheimer's disease. Tau undergoes several post-translational modifications of which phosphorylation and O-GlcNAcylation are key chemical modifications. Tau aggregates into paired helical filaments and neurofibrillary tangles upon hyperphosphorylation, whereas O-GlcNAcylation stabilizes the soluble form of Tau. How specific phosphorylation and/or O-GlcNAcylation events influence Tau conformations remains largely unknown due to the disordered nature of Tau. In this study, we have investigated the phosphorylation- and O-GlcNAcylation-induced conformational effects on a Tau segment (Tau225-246) from the proline-rich domain (P2), by performing metadynamics simulations. We study two different phosphorylation patterns: Tau225-246, phosphorylated at T231 and S235, and Tau225-246, phosphorylated at T231, S235, S237, and S238. We also study O-GlcNAcylation at T231 and S235. We find that phosphorylation leads to the formation of strong salt-bridge contacts with adjacent lysine and arginine residues, which disrupts the native β-sheet structure observed in Tau225-246. We also observe the formation of a transient α-helix (238SAKSRLQ244) when Tau225-246 is phosphorylated at four sites. In contrast, O-GlcNAcylation shows only modest structural effects, and the resultant structure resembles the native form of the peptide. Our studies suggest the opposing structural effects of both protein post-translational modifications (PTMs) and the importance of salt bridges in governing the conformational preferences upon phosphorylation, highlighting the role of proximal arginine and lysine upon hyperphosphorylation.
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Affiliation(s)
- Lata Rani
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar382355, Gujarat, India
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania18015, United States
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar382355, Gujarat, India
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Pandey P, Aytenfisu AH, MacKerell AD, Mallajosyula SS. Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives. J Chem Theory Comput 2019; 15:4982-5000. [PMID: 31411469 PMCID: PMC6852669 DOI: 10.1021/acs.jctc.9b00327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we report the development of Drude polarizable force field parameters for the carboxylate and N-acetyl amine derivatives, extending the functionality of the existing Drude polarizable carbohydrate force field. The force field parameters have been developed in a hierarchical manner, reproducing the quantum mechanical gas-phase properties of small model compounds representing the key functional group in the carbohydrate derivatives, including optimization of the electrostatic and bonded parameters. The optimized parameters were then used to generate the models for carboxylate and N-acetyl amine carbohydrate derivatives. The transferred parameters were further tested and optimized to reproduce crystal geometries and J-coupling data from nuclear magnetic resonance experiments. The parameter development resulted in the incorporation of d-glucuronate, l-iduronate, N-acetyl-d-glucosamine (GlcNAc), and N-acetyl-d-galactosamine (GalNAc) sugars into the Drude polarizable force field. The parameters developed in this study were then applied to study the conformational properties of glycosaminoglycan polymer hyaluronan, composed of d-glucuronate and N-acetyl-d-glucosamine, in aqueous solution. Upon comparing the results from the additive and polarizable simulations, it was found that the inclusion of polarization improved the description of the electrostatic interactions observed in hyaluronan, resulting in enhanced conformational flexibility. The developed Drude polarizable force field parameters in conjunction with the remainder of the Drude polarizable force field parameters can be used for future studies involving carbohydrates and their conjugates in complex, heterogeneous systems.
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Affiliation(s)
| | - Asaminew H Aytenfisu
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
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Sanghavi HM, Mallajosyula SS, Majumdar S. Correction to: Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region. BMC Struct Biol 2019; 19:7. [PMID: 30925869 PMCID: PMC6441143 DOI: 10.1186/s12900-019-0105-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 05/30/2023]
Affiliation(s)
- Hiral M Sanghavi
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Sharmistha Majumdar
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India.
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Affiliation(s)
- Amita Sihag
- Department of ChemistryIndian Institute of Technology Gandhinagar Palaj, Gandhinagar Gujrat – 382355 India
| | - Sairam S. Mallajosyula
- Department of ChemistryIndian Institute of Technology Gandhinagar Palaj, Gandhinagar Gujrat – 382355 India
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Sanghavi HM, Mallajosyula SS, Majumdar S. Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region. BMC Struct Biol 2019; 19:4. [PMID: 30836974 PMCID: PMC6402169 DOI: 10.1186/s12900-019-0102-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 01/29/2019] [Indexed: 12/22/2022]
Abstract
Background The THAP (Thanatos Associated Proteins) protein family in humans is implicated in various important cellular processes like epigenetic regulation, maintenance of pluripotency, transposition and disorders like cancers and hemophilia. The human THAP protein family which consists of twelve members of different lengths has a well characterized amino terminal, zinc-coordinating, DNA-binding domain called the THAP domain. However, the carboxy terminus of most THAP proteins is yet to be structurally characterized. A coiled coil region is known to help in protein oligomerization in THAP1 and THAP11. It is not known if other human THAP proteins oligomerize. We have used bioinformatic tools to explore the possibility of dimerization of THAP proteins via a coiled coil region. Results Classification of human THAP protein into three size based groups led to the identification of an evolutionarily conserved alpha helical region, downstream of the amino terminal THAP domain. Secondary structure predictions, alpha helical wheel plots and protein models demonstrated the strong possibility of coiled coil formation in this conserved, leucine rich region of all THAP proteins except THAP10. Conclusions The identification of a predicted oligomerization region in the human THAP protein family opens new directions to investigate the members of this protein family. Electronic supplementary material The online version of this article (10.1186/s12900-019-0102-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiral M Sanghavi
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Sharmistha Majumdar
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India.
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Abstract
Antifreeze glycoproteins (AFGPs) are distinctively riveting class of bio-macromolecules, which endows the survival of organisms inhabiting polar and subpolar regions. These proteins are believed to hinder microscopic freezing by interacting with embryonic ice crystals and precluding their further growth. The underlying molecular mechanism by which AFGPs bind to ice has remained elusive due to insufficient structural characterization, with conflicting hypotheses on the possible binding mode of AFGPs - either via the hydrophobic peptide backbone or via the hydrophilic carbohydrate side chains - when interacting with ice. Chemical synthesis has allowed researchers to access synthetic variants of natural AFGPs. These studies revealed that AFGPs exhibit huge variations in their thermal hysteresis and ice shaping behavior with only slight structural variations, especially to the carbohydrate side chains. Four key structural motifs were identified as crucial to AFGP activity: the presence of a threonine γ-methyl group, an α-glycosidic carbohydrate-protein linkage, an acetylamide group (-NHCOCH3) at the C2 position of the carbohydrate linked to the protein, and the presence of carbohydrate hydroxyl groups. In this study, we use molecular dynamics (MD) simulations to probe the microscopic properties of water accompanying these structural variations of AFGPs. We find that these variations primarily influence the conformation space of AFGPs and also crucially control their hydration dynamics. Owing to the disordered nature of AFGPs we use Markov-state modeling to identify the conformational preferences of AFGPs. The simulations reveal the importance of steric bulk, intra-molecular carbohydrate-protein H-bonds and conformational preferences (α- vs. β-linkages) in controlling the spatial segregation of the hydrophilic and hydrophobic regions of AFGPs. We hypothesize that the hydrophobic component of AFGPs is crucial to their binding to ice, which determines the ice shaping ability of AFGPs. However, the hydrophilic carbohydrate hydroxyl groups and their ability to form water bridges control the subsequent hydration dynamics, which is key to the antifreeze properties. Investigating the tetrahedral order parameter of water molecules around the carbohydrates revealed competition between solute- and bulk-influenced solvent structures, with maximum restructuring being observed in the interfacial region 2.5-4.5 Å away from the AFGPs.
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Affiliation(s)
- Poonam Pandey
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Simkheda, Gandhinagar, Gujarat, India.
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Kumari B, Singh SP, Santosh R, Dutta A, Mallajosyula SS, Ghosal S, Kanvah S. Branching effect on triphenylamine-CF3 cyanostilbenes: enhanced emission and aggregation in water. NEW J CHEM 2019. [DOI: 10.1039/c8nj05907a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aggregation-induced emission and gelation behavior of symmetric and asymmetric triphenylamines
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Affiliation(s)
- Beena Kumari
- Department of Chemistry, Indian Institute of Technology Gandhinagar
- Gandhinagar 382 355
- India
| | - Surya Pratap Singh
- Department of Chemistry, Indian Institute of Technology Gandhinagar
- Gandhinagar 382 355
- India
| | - Ranga Santosh
- Department of Chemistry
- Birla Institute of Technology Pilani Hyderabad Campus
- Hyderabad
- India
| | - Arnab Dutta
- Department of Chemistry, Indian Institute of Technology Gandhinagar
- Gandhinagar 382 355
- India
| | - Sairam S. Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar
- Gandhinagar 382 355
- India
| | - Subhas Ghosal
- Department of Chemistry
- National Institute of Technology
- Durgapur 713209, WB
- India
| | - Sriram Kanvah
- Department of Chemistry, Indian Institute of Technology Gandhinagar
- Gandhinagar 382 355
- India
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Pandey P, Patel V, George NV, Mallajosyula SS. KELM-CPPpred: Kernel Extreme Learning Machine Based Prediction Model for Cell-Penetrating Peptides. J Proteome Res 2018; 17:3214-3222. [DOI: 10.1021/acs.jproteome.8b00322] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Poonam Pandey
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Ahmedabad, Gujarat 382355, India
| | - Vinal Patel
- Department of Electrical Engineering, Indian Institute of Technology Gandhinagar, Ahmedabad, Gujarat 382355, India
| | - Nithin V. George
- Department of Electrical Engineering, Indian Institute of Technology Gandhinagar, Ahmedabad, Gujarat 382355, India
| | - Sairam S. Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Ahmedabad, Gujarat 382355, India
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16
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Abstract
Dimeric cyanine dyes self-assemble into H-dimers and H-aggregates, which experience de-aggregation with specific biomolecules.
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Affiliation(s)
- Prathap Reddy Patlolla
- Department of Chemistry
- Indian Institute of Technology Gandhinagar
- Palaj
- Gandhinagar 382355
- India
| | - Amarjyoti Das Mahapatra
- Department of Chemistry
- Indian Institute of Technology Gandhinagar
- Palaj
- Gandhinagar 382355
- India
| | - Sairam S. Mallajosyula
- Department of Chemistry
- Indian Institute of Technology Gandhinagar
- Palaj
- Gandhinagar 382355
- India
| | - Bhaskar Datta
- Department of Chemistry
- Indian Institute of Technology Gandhinagar
- Palaj
- Gandhinagar 382355
- India
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Affiliation(s)
- Prathap Reddy Patlolla
- Department of Chemistry; Indian Institute of Technology Gandhinagar; Palaj, Gandhinagar 382355 India, Phone: 079-2395-2073, Fax: 079-2397-2622
| | - Sairam S. Mallajosyula
- Department of Chemistry; Indian Institute of Technology Gandhinagar; Palaj, Gandhinagar 382355 India, Phone: 079-2395-2073, Fax: 079-2397-2622
| | - Bhaskar Datta
- Department of Chemistry; Indian Institute of Technology Gandhinagar; Palaj, Gandhinagar 382355 India, Phone: 079-2395-2073, Fax: 079-2397-2622
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18
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Rani L, Mallajosyula SS. Phosphorylation versus O-GlcNAcylation: Computational Insights into the Differential Influences of the Two Competitive Post-Translational Modifications. J Phys Chem B 2017; 121:10618-10638. [DOI: 10.1021/acs.jpcb.7b08790] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Lata Rani
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India - 382355
| | - Sairam S. Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India - 382355
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Wu EL, Qi Y, Park S, Mallajosyula SS, MacKerell AD, Klauda JB, Im W. Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophys J 2016; 109:2090-100. [PMID: 26588568 DOI: 10.1016/j.bpj.2015.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/04/2015] [Accepted: 10/08/2015] [Indexed: 11/29/2022] Open
Abstract
Prion diseases are fatal neurodegenerative disorders, which are characterized by the accumulation of misfolded prion protein (PrPSc) converted from a normal host cellular prion protein (PrPC). Experimental studies suggest that PrPC is enriched with α-helical structure, whereas PrPSc contains a high proportion of β-sheet. In this study, we report the impact of N-glycosylation and the membrane on the secondary structure stability utilizing extensive microsecond molecular dynamics simulations. Our results reveal that the HB (residues 173 to 194) C-terminal fragment undergoes conformational changes and helix unfolding in the absence of membrane environments because of the competition between protein backbone intramolecular and protein-water intermolecular hydrogen bonds as well as its intrinsic instability originated from the amino acid sequence. This initiation of the unfolding process of PrPC leads to a subsequent increase in the length of the HB-HC loop (residues 195 to 199) that may trigger larger rigid body motions or further unfolding around this region. Continuous interactions between prion protein and the membrane not only constrain the protein conformation but also decrease the solvent accessibility of the backbone atoms, thereby stabilizing the secondary structure, which is enhanced by N-glycosylation via additional interactions between the N-glycans and the membrane surface.
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Affiliation(s)
- Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Soohyung Park
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Sairam S Mallajosyula
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland; Department of Chemistry, Indian Institute of Technology Gandhinagar, Chandkheda, Ahmedabad, Gujarat, India
| | - Alexander D MacKerell
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Chandkheda, Ahmedabad, Gujarat, India
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, The University of Maryland, College Park, Maryland
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas.
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Pandey P, Mallajosyula SS. Influence of Polarization on Carbohydrate Hydration: A Comparative Study Using Additive and Polarizable Force Fields. J Phys Chem B 2016; 120:6621-33. [PMID: 27266974 DOI: 10.1021/acs.jpcb.6b05546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Carbohydrates are known to closely modulate their surrounding solvent structures and influence solvation dynamics. Spectroscopic investigations studying far-IR regions (below 1000 cm(-1)) have observed spectral shifts in the libration band (around 600 cm(-1)) of water in the presence of monosaccharides and polysaccharides. In this paper, we use molecular dynamics simulations to gain atomistic insight into carbohydrate-water interactions and to specifically highlight the differences between additive (nonpolarizable) and polarizable simulations. A total of six monosaccharide systems, α and β anomers of glucose, galactose, and mannose, were studied using additive and polarizable Chemistry at HARvard Macromolecular Mechanics (CHARMM) carbohydrate force fields. Solvents were modeled using three additive water models TIP3P, TIP4P, and TIP5P in additive simulations and polarizable water model SWM4 in polarizable simulations. The presence of carbohydrate has a significant effect on the microscopic water structure, with the effects being pronounced for proximal water molecules. Notably, disruption of the tetrahedral arrangement of proximal water molecules was observed due to the formation of strong carbohydrate-water hydrogen bonds in both additive and polarizable simulations. However, the inclusion of polarization resulted in significant water-bridge occupancies, improved ordered water structures (tetrahedral order parameter), and longer carbohydrate-water H-bond correlations as compared to those for additive simulations. Additionally, polarizable simulations also allowed the calculation of power spectra from the dipole-dipole autocorrelation function, which corresponds to the IR spectra. From the power spectra, we could identify spectral signatures differentiating the proximal and bulk water structures, which could not be captured from additive simulations.
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Affiliation(s)
- Poonam Pandey
- Department of Chemistry, Indian Institute of Technology Gandhinagar , Simkheda, Gandhinagar, Gujarat 382355, India
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar , Simkheda, Gandhinagar, Gujarat 382355, India
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21
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Abstract
Molecular dynamics simulations are an effective tool to study the structure, dynamics, and thermodynamics of carbohydrates and proteins. However, the simulations of heterogeneous glycoprotein systems have been limited due to the lack of appropriate molecular force field parameters describing the linkage between the carbohydrate and the protein regions as well as the tools to prepare these systems for modeling studies. In this work we outline the recent developments in the CHARMM carbohydrate force field to treat glycoproteins and describe in detail the step-by-step procedures involved in building glycoprotein geometries using CHARMM-GUI Glycan Reader.
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Affiliation(s)
- Sairam S. Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Sunhwan Jo
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive Lawrence, KS 66047, USA
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive Lawrence, KS 66047, USA
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
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22
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Mallajosyula SS, Vanommeslaeghe K, MacKerell AD. Perturbation of long-range water dynamics as the mechanism for the antifreeze activity of antifreeze glycoprotein. J Phys Chem B 2014; 118:11696-706. [PMID: 25137353 PMCID: PMC4191590 DOI: 10.1021/jp508128d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Very little is known about the mechanism of antifreeze action of antifreeze glycoproteins (AFGPs) present in Antarctic teleost fish. Recent NMR and CD studies assisted with total synthesis of synthetic AFGP variants have provided insight into the structure of short AFGP glycopeptides, though the observations did not yield information on the antifreeze mechanism of action. In this study, we use Hamiltonian replica exchange (HREX) molecular dynamics simulations to probe the structure and surrounding aqueous environments of both the natural (AFGP8) and synthetic (s-AFGP4) AFGPs. AFGPs can adopt both amphiphilic and pseudoamphiphilic conformations, the preference of which is related to the proline content of the peptide. The arrangement of carbohydrates allows the hydroxyl groups on terminal galactose units to form stable water bridges which in turn influence the hydrogen-bond network, structure, and dynamics of the surrounding solvent. Interestingly, these local effects lead to the perturbation of the tetrahedral environment for water molecules in hydration layers far (10.0-12.0 Å) from the AFGPs. This structure-induced alteration of long-range hydration dynamics is proposed to be the major contributor to antifreeze activity, a conclusion that is in line with terahertz spectroscopy experiments. The detailed structure-mechanism correlation provided in this study could lead to the design of better synthetic AFGP variants.
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Affiliation(s)
- Sairam S Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland , 20 Penn Street HSF II, Baltimore, Maryland 21201, United States
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23
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Patel DS, Pendrill R, Mallajosyula SS, Widmalm G, MacKerell AD. Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments. J Phys Chem B 2014; 118:2851-71. [PMID: 24552401 PMCID: PMC3979472 DOI: 10.1021/jp412051v] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Conformational sampling for a set of 10 α- or β-(1→6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton-proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated (3)J(H5,H6R) values from the experimental data, prompting optimization of the ω torsion angle parameters associated with (1→6)-linkages. The resulting force field is in overall good agreement (i.e., within ∼0.5 Hz deviation) from experimental (3)J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6···HO2' hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the ω torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1→6)-linkage as compared to the O6' atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of ω torsion angles in oligosaccharides is also explored.
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Affiliation(s)
- Dhilon S Patel
- Department of Pharmaceutical Sciences, University of Maryland , 20 Penn Street HSF II, Baltimore, Maryland 21201, United States
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Sabit H, Mallajosyula SS, MacKerell AD, Swaan PW. Transmembrane domain II of the human bile acid transporter SLC10A2 coordinates sodium translocation. J Biol Chem 2013; 288:32394-32404. [PMID: 24045943 DOI: 10.1074/jbc.m113.518555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human apical sodium-dependent bile acid transporter (hASBT, SLC10A2) is responsible for intestinal reabsorption of bile acids and plays a key role in cholesterol homeostasis. We used a targeted and systematic approach to delineate the role of highly conserved transmembrane helix 2 on the expression and function of hASBT. Cysteine mutation significantly depressed transport activity for >60% of mutants without affecting cell surface localization of the transporter. All mutants were inaccessible toward chemical modification by membrane-impermeant MTSET reagent, strongly suggesting that transmembrane 2 (TM2) plays an indirect role in bile acid substrate translocation. Both bile acid uptake and sodium dependence of TM2 mutants revealed a distinct α-helical periodicity. Kinetic studies with conservative and non-conservative mutants of sodium sensitive residues further underscored the importance of Gln(75), Phe(76), Met(79), Gly(83), Leu(86), Phe(90), and Asp(91) in hASBT function. Computational analysis indicated that Asp(91) may coordinate with sodium during the transport cycle. Combined, our data propose that a consortium of sodium-sensitive residues along with previously reported residues (Thr(134), Leu(138), and Thr(149)) from TM3 may form the sodium binding and translocation pathway. Notably, residues Gln(75), Met(79), Thr(82), and Leu(86) from TM2 are highly conserved in TM3 of a putative remote bacterial homologue (ASBTNM), suggesting a universal mechanism for the SLC10A transporter family.
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Affiliation(s)
- Hairat Sabit
- From the Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201
| | - Sairam S Mallajosyula
- From the Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D MacKerell
- From the Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201
| | - Peter W Swaan
- From the Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201.
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25
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Mallajosyula SS, Adams KM, Barchi JJ, MacKerell AD. Conformational determinants of the activity of antiproliferative factor glycopeptide. J Chem Inf Model 2013; 53:1127-37. [PMID: 23627670 DOI: 10.1021/ci400147s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core 1 α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic APF provided a platform to study amino acid modifications and their effect on APF activity, based on which a structure-activity relationship (SAR) for APF activity was previously proposed. However, this SAR model could not explain the change in activity associated with minor alterations in the peptide sequence. Presented is computational analysis of 14 APF derivatives to identify structural trends from which a more detailed SAR is obtained. The APF activity is found to be dictated by the close interplay between carbohydrate-peptide and peptide-peptide interactions. The former involves hydrogen bond and hydrophobic interactions, and the latter is dominated by hydrophobic interactions. The highly flexible hydrophobic peptide adopts collapsed conformations separated by low energy barriers. APF activity correlates with hydrophobic clustering associated with amino acids 4A, 6V, and 8V. Peptide conformations are highly sensitive to single point mutations, which explain the experimental trends. The presented SAR will act as a guide for lead optimization of more potent APF analogues of potential therapeutic utility.
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Affiliation(s)
- Sairam S Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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26
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Mallajosyula SS, Guvench O, Hatcher E, MacKerell AD. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates. J Chem Theory Comput 2012; 8:759-776. [PMID: 22685386 PMCID: PMC3367516 DOI: 10.1021/ct200792v] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presented is an extension of the CHARMM additive all-atom carbohydrate force field to enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates. Target data for parameter optimization included full two-dimensional energy surfaces defined by the glycosidic dihedral angle pairs in the phosphate/sulfate model compound analogs of hexopyranose monosaccharide phosphates and sulfates, as determined by quantum mechanical (QM) MP2/cc-pVTZ single point energies on MP2/6-31+G(d) optimized structures. In order to achieve balanced, transferable dihedral parameters for the dihedral angles, surfaces for all possible anomeric and conformational states were included during the parametrization process. In addition, to model physiologically relevant systems both the mono- and di-anionic charged states were studied for the phosphates. This resulted in over 7000 MP2/cc-pVTZ//MP2/6-31G+(d) model compound conformational energies which, supplemented with QM geometries, were the main target data for the parametrization. Parameters were validated against crystals of relevant monosaccharide derivatives obtained from the Cambridge Structural Database (CSD) and larger systems, namely inositol-(tri/tetra/penta) phosphates non-covalently bound to the pleckstrin homology (PH) domain and oligomeric chondroitin sulfate in solution and in complex with cathepsin K protein.
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Affiliation(s)
- Sairam S. Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, Portland, Maine 04103
| | - Elizabeth Hatcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
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27
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Guvench O, Mallajosyula SS, Raman EP, Hatcher E, Vanommeslaeghe K, Foster TJ, Jamison FW, MacKerell AD. CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling. J Chem Theory Comput 2011; 7:3162-3180. [PMID: 22125473 PMCID: PMC3224046 DOI: 10.1021/ct200328p] [Citation(s) in RCA: 435] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, Portland, Maine 04103
| | - Sairam S. Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - E. Prabhu Raman
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Elizabeth Hatcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Theresa J. Foster
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, Portland, Maine 04103
| | - Francis W. Jamison
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, Portland, Maine 04103
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
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28
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Abstract
A detailed investigation of the conformational properties of all the biologically relevant O-glycosidic linkages using the Hamiltonian replica exchange (HREX) simulation methodology and the recently developed CHARMM carbohydrate force field parameters is presented. Fourteen biologically relevant O-linkages between the five sugars N-acetylgalactosamine (GalNAc), N-acetylglucosamine (GlcNAc), D-glucose (Glc), D-mannose (Man), and L-fucose (Fuc) and the amino acids serine and threonine were studied. The force field was tested by comparing the simulation results of the model glycopeptides to various NMR (3)J coupling constants, NOE distances, and data from molecular dynamics with time-averaged restraints (tar-MD). The results show the force field to be in overall agreement with experimental and previous tar-MD simulations, although some small limitations are identified. An in-depth hydrogen bond and bridging water analysis revealed an interplay of hydrogen bonding and bridge water interactions influencing the geometry of the underlying peptide backbone, with the O-linkages favoring extended β-sheet and polyproline type II (PPII) conformations over the compact α(R)-helical conformation. The newly developed parameters were also able to identify hydrogen bonding and water mediated interactions between O-linked sugars and proteins. These results indicate that the newly developed parameters in tandem with HREX conformational sampling provide the means to study glycoproteins in the absence of targeted NMR restraint data.
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Affiliation(s)
- Sairam S. Mallajosyula
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
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29
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Abstract
The alignment of Cu(2+) ions along a modified DNA helix is studied with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S-en) metalated base pairs (MBPs). The conformational motion of H-MBP leads to the interlinking of the H-MBPs by an extended Cu-O network that is ferromagnetic, whereas the conformational freezing of the S-en-MBP leads to an ordered pairwise-stacked arrangement that is weakly antoferrimagnetic.
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Affiliation(s)
- Sairam S Mallajosyula
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
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30
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Mallajosyula SS, Gupta A, Pati SK. Fluctuations at the Base Pair Level Effecting Charge Transfer in DNA. J Phys Chem A 2009. [DOI: 10.1021/jp905403h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Affiliation(s)
- Sairam S. Mallajosyula
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India, and Department of Chemistry, Udai Pratap Autonomous College, Varanasi, Uttar Pradesh 221002, India
| | - Ashutosh Gupta
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India, and Department of Chemistry, Udai Pratap Autonomous College, Varanasi, Uttar Pradesh 221002, India
| | - Swapan K. Pati
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India, and Department of Chemistry, Udai Pratap Autonomous College, Varanasi, Uttar Pradesh 221002, India
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Mallajosyula SS, Usha H, Datta A, Pati SK. Molecular modelling of a chemodosimeter for the selective detection of As(III) ion in water. J CHEM SCI 2009. [DOI: 10.1007/s12039-008-0095-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Mallajosyula SS, Parida P, Pati SK. Organometallic vanadium-borazine systems: efficient one-dimensional half-metallic spin filters. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b810089f] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mallajosyula SS, Pati SK. Benzimidazole-Modified Single-Stranded DNA: Stable Scaffolds for 1-Dimensional Spintronics Constructs. J Phys Chem B 2008; 112:16982-9. [DOI: 10.1021/jp8080782] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sairam S. Mallajosyula
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Centre For Advanced Scientific Research, Jakkur, Bangalore, India 560064
| | - Swapan K. Pati
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Centre For Advanced Scientific Research, Jakkur, Bangalore, India 560064
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35
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Mallajosyula SS, Lin JC, Cox DL, Pati SK, Singh RRP. Sequence dependent electron transport in wet DNA: ab initio and molecular dynamics studies. Phys Rev Lett 2008; 101:176805. [PMID: 18999773 DOI: 10.1103/physrevlett.101.176805] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Indexed: 05/27/2023]
Abstract
We combine molecular dynamics simulations and density functional theory to analyze the electrical structure and transmission probability in four different DNA sequences under physiological conditions. The conductance in these sequences is primarily controlled by interstrand and intrastrand coupling between low-energy guanine orbitals. Insertion of adenine-thymine base pairs between the guanine-cytosine rich domains acts as a tunneling barrier. Our theory explains recent length dependent conductance data for individual DNA molecules in water.
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Affiliation(s)
- Sairam S Mallajosyula
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore, India
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36
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Affiliation(s)
- Sairam S. Mallajosyula
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Centre For Advanced Scientific Research, Jakkur Campus, Bangalore 560064, India
| | - Swapan K Pati
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Centre For Advanced Scientific Research, Jakkur Campus, Bangalore 560064, India
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37
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Abstract
Protonation of DNA basepairs is a reversible phenomenon that can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen-bonding pattern of the DNA basepairs undergoes a change. We study the effect of protonation on the electronic properties of the DNA basepairs to probe for possible molecular electronics applications. We find that, under mild acidic pH conditions, the A:T basepair shows excellent rectification behavior that is, however, absent in the G:C basepair. The mechanism of rectification has been discussed using a simple chemical potential model. We also consider the noncanonical A:A basepair and find that it can be used as efficient pH dependent molecular switch. The switching action in the A:A basepair is explained in the light of pi-pi interactions, which lead to efficient delocalization over the entire basepair.
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Affiliation(s)
- Sairam S Mallajosyula
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore, India
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38
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Abstract
Motivated by recent experiments we study the alignment of magnetic ions Cu2+ and Mn2+ along the modified DNA helix. We find that doping with magnetic ions induces conducting states in the gap region of natural DNA. These magnetic ions are found to interact ferromagnetically along the DNA helix. Calculations of optical conductivity about the helical axis suggest that the origin of magnetic characteristics depend on the metal ions; while Cu-DNA favors in-plane sigma-like delocalization over the base pairs, the Mn-DNA favors out-of-plane (pi) delocalizations. Such an alignment of magnetic ions offers promising perspectives for creating low-dimensional polarized spin channel within the DNA helix.
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Affiliation(s)
- Sairam S Mallajosyula
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
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39
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Datta A, Mallajosyula SS, Pati SK. Nonlocal electronic distribution in metallic clusters: a critical examination of aromatic stabilization. Acc Chem Res 2007; 40:213-21. [PMID: 17370993 DOI: 10.1021/ar0682738] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All-metal clusters, such as Al(4)M(4) (M = alkali metal ion), exhibit interesting features of multi-fold aromaticity/antiaromaticity. Such characteristics arise particularly because of the poor sigma-pi separation in this class of systems. This Account presents computational strategies to unambiguously determine the aromaticity/antiaromaticity characteristics of such clusters. Computations of the linear and nonlinear optical responses show that all-metal clusters are orders of magnitude more polarized than the conventional pi-conjugated molecules. We also propose new strategies to stabilize all-metal antiaromatic systems through complexation to transition metals and discuss mechanisms for substitution reactions within the conventional organometallic systems by Al(4)M(4). Additionally, we find that these all-metal clusters form stacked superclusters that are extremely stable and aromatic.
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Affiliation(s)
- Ayan Datta
- Theoretical Sciences Unit, Chemistry and Physics of Materials Unit and DST Unit on Nanoscience, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
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Mallajosyula SS, Datta A, Pati SK. Aromatic Superclusters from All-Metal Aromatic and Antiaromatic Monomers, [Al4]2-and [Al4]4-. J Phys Chem B 2006; 110:20098-101. [PMID: 17034180 DOI: 10.1021/jp064821n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Calculations on the structures of dimers of all-metal aromatic and anti-aromatic molecules such as (Al4(2-)) and (Al4(4-)) reveal that, unlike their organic counterparts such as benzene and cyclobutadiene which form pi-stacked complexes, these molecules form new clusters with no reminiscence of the original units. These clusters have a very large binding energy and can be further stabilized through charge-balance by counterions and solvents.
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Mohan PJ, Datta A, Mallajosyula SS, Pati SK. Structures of Nucleobases Trapped within Au Triangles and Its Effects on Hydrogen Bonding in Base Pairs of DNA. J Phys Chem B 2006; 110:18661-4. [PMID: 16970496 DOI: 10.1021/jp0639041] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleobases (adenine (A), thymine (T), cytosine (C), and guanine (G)) trapped within two metal clusters such as Au(3) undergo expansion. Our investigation reveals that this primarily arises due to the concomitant increase in all the bond lengths in molecules. Such expansion of the molecules can be qualitatively understood on the basis of classical harmonic potentials in the bonds and loss of aromaticity in the rings. Specifically, the highly electronegative O and N elements in the base pairs anchor to Au atoms and form X-Au bonds, which leads to charge redistribution within the molecules. As a very important consequence of this, the nature of the hydrogen bonds (in Au(3)-A...T-Au(3) and in Au(3)-G...C-Au(3)) change substantially within these electrodes in comparison to gas-phase structures. These hydrogen bonds have a single-well potential energy profile (of the type N...H...O and N...H...N) instead of double-well potentials (like N-H...O or N-H...N/ N...H-N types). A detailed energy calculation along the proton movement pathway supports our conclusions.
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Affiliation(s)
- P J Mohan
- Theoretical Sciences Unit, Chemistry and Physics of Materials Unit, and the DST Unit on Nanoscience, Jawaharlal Nehru Center for Advcanced Scientific Research, Jakkur Campus, Bangalore, India
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Mallajosyula SS, Datta A, Pati SK. Conformational Preference in Heteroatomic Analogues of Ethane, H3X−YH3 (X = B, Al; Y = N, P): Implications of Charge Transfer. J Phys Chem A 2006; 110:5156-63. [PMID: 16610839 DOI: 10.1021/jp0575761] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum chemical conformational analysis for electron donor-acceptor (EDA) systems, H3B-NH3, H3B-PH3, H3Al-NH3 and H3Al-PH3, has been performed. For H3B-NH3 and H3B-PH3, the rotational barrier is found to be invariant with an increase in the central bond (X-Y) length. For H3Al-NH3 and H3Al-PH3, however, the rotational barrier increases with an increase in the central bond length. Decomposition of the total energy into various components and their contributions to the frontier orbitals (HOMO, HOMO-1, HOMO-2 and HOMO-3) have been analyzed in detail to explain the origin of such anomalous changes in the rotational barrier. Charge transfer and favorable "back bonding" are found to be the crucial factors governing the variations in the rotational barrier for such systems.
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Affiliation(s)
- Sairam S Mallajosyula
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
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Rehaman A, Datta A, Mallajosyula SS, Pati SK. Quantifying Aromaticity at the Molecular and Supramolecular Limits: Comparing Homonuclear, Heteronuclear, and H-Bonded Systems. J Chem Theory Comput 2005; 2:30-6. [DOI: 10.1021/ct0501598] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abdul Rehaman
- Theoretical Sciences Unit and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
| | - Ayan Datta
- Theoretical Sciences Unit and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
| | - Sairam S. Mallajosyula
- Theoretical Sciences Unit and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
| | - Swapan K. Pati
- Theoretical Sciences Unit and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
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