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13 results on '"Narwani Tarun Jairaj"'

1. Dynamics and deformability of α-, 310- and π-helices

Author

Narwani Tarun Jairaj, Craveur Pierrick, Shinada Nicolas K., Santuz Hubert, Rebehmed Joseph, Etchebest Catherine, and de Brevern Alexandre G.

Subjects
helical local conformations, structural alphabet, molecular dynamics, disorder, flexibility, Biology (General), QH301-705.5
Abstract

Protein structures are often represented as seen in crystals as (i) rigid macromolecules (ii) with helices, sheets and coils. However, both definitions are partial because (i) proteins are highly dynamic macromolecules and (ii) the description of protein structures could be more precise. With regard to these two points, we analyzed and quantified the stability of helices by considering α-helices as well as 310- and π-helices. Molecular dynamic (MD) simulations were performed on a large set of 169 representative protein domains. The local protein conformations were followed during each simulation and analyzed. The classical flexibility index (B-factor) was confronted with the MD root mean square flexibility (RMSF) index. Helical regions were classified according to their level of helicity from high to none. For the first time, a precise quantification showed the percentage of rigid and flexible helices that underlie unexpected behaviors. Only 76.4% of the residues associated with α-helices retain the conformation, while this tendency drops to 40.5% for 310-helices and is never observed for π-helices. α-helix residues that do not remain as an α-helix have a higher tendency to assume β-turn conformations than 310- or π-helices. The 310-helices that switch to the α-helix conformation have a higher B-factor and RMSF values than the average 310-helix but are associated with a lower accessibility. Rare π-helices assume a β-turn, bend and coil conformations, but not α- or 310-helices. The view on π-helices drastically changes with the new DSSP (Dictionary of Secondary Structure of Proteins) assignment approach, leading to behavior similar to 310-helices, thus underlining the importance of secondary structure assignment methods.

Published
2018
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5. Recent advances on polyproline II

Author

Narwani, Tarun Jairaj, Santuz, Hubert, Shinada, Nicolas, Melarkode Vattekatte, Akhila, Ghouzam, Yassine, Srinivasan, Narayanasamy, Gelly, Jean-Christophe, and de Brevern, Alexandre G.

Published
2017
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6. Data set of intrinsically disordered proteins analysed at a local protein conformation level

Author

Melarkode Vattekatte, Akhila, Narwani, Tarun Jairaj, Floch, Aline, Maljković, Mirjana, Bisoo, Soubika, Shinada, Nicolas Ken, Kranjc, Agata, Gelly, Jean-Christophe, Srinivasan, Narayanaswamy, Mitić, Nenad, de Brevern, Alexandre, Institut National de la Transfusion Sanguine [Paris] (INTS), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), University of Belgrade [Belgrade, Serbie] (Faculty of Mathematics), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP), Discngine S.A.S [Paris], SBX corp, Molecular Biophysics Unit, Indian Institute of Science, Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), University of Belgrade [Belgrade], Molecular Biophysics Unit [Bangalore, India] (IISc), Indian Institute of Science [Bangalore] (IISc Bangalore), de Brevern, Alexandre G., and Univ, Réunion

Subjects
PDB, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Structural alphabet, Entropy, [SDV]Life Sciences [q-bio], Local protein conformation, lcsh:Computer applications to medicine. Medical informatics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV] Life Sciences [q-bio], Biochemistry, Genetics and Molecular Biology, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, lcsh:R858-859.7, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Protein disorder, Ensembles, lcsh:Science (General), lcsh:Q1-390
Abstract

Intrinsic Disorder Proteins (IDPs) have become a hot topic since their characterisation in the 90s. The data presented in this article are related to our research entitled “A structural entropy index to analyse local conformations in Intrinsically Disordered Proteins” published in Journal of Structural Biology [1]. In this study, we quantified, for the first time, continuum from rigidity to flexibility and finally disorder. Non-disordered regions were also highlighted in the ensemble of disordered proteins. This work was done using the Protein Ensemble Database (PED), which is a useful database collecting series of protein structures considered as IDPs. The data set consists of a collection of cleaned protein files in classical pdb format that can be readily used as an input with most automatic analysis software. The accompanying data include the coding of all structural information in terms of a structural alphabet, namely Protein Blocks (PBs). An entropy index derived from PBs that allows apprehending the continuum between protein rigidity to flexibility to disorder is included, with information from secondary structure assignment, protein accessibility and prediction of disorder from the sequences. The data may be used for further structural bioinformatics studies of IDPs. It can also be used as a benchmark for evaluating disorder prediction methods. Keywords: Protein disorder, PDB, Ensembles, Entropy, Local protein conformation, Structural alphabet

Published
2020

7. A structural entropy index to analyse local conformations in intrinsically disordered proteins: IDP PBs

Author

Melarkode Vattekatte, Akhila, Narwani, Tarun Jairaj, Floch, Aline, Maljković, Mirjana, Bisoo, Soubika, Shinada, Nicolas, Kranjc, Agata, Gelly, Jean-Christophe, Srinivasan, Narayanaswamy, Mitić, Nenad, de Brevern, Alexandre, de Brevern, Alexandre G., Université de Paris - - Université de Paris2018 - ANR-18-IDEX-0001 - IDEX - VALID, Université Sorbonne Paris Cité - - USPC2011 - ANR-11-IDEX-0005 - IDEX - VALID, Institut National de la Transfusion Sanguine [Paris] (INTS), Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), University of Belgrade, Faculty of Mathematics, Molecular Biophysics Unit, Indian Institute of Science, Discngine S.A.S [Paris], Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. c2013037147 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., Conseil Régional Ile de France. INTS (SESAME Grant)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), and ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011)

Subjects
flexibility, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], rigidity, protein structures, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, structural alphabet, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, entropy, Condensed Matter::Disordered Systems and Neural Networks, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract

International audience; Sequence – structure – function paradigm has been revolutionized by the discovery of disordered regions and disordered proteins more than two decades ago. While the definition of rigidity is simple with X-ray structures, the notion of flexibility is linked to high experimental B-factors. The definition of disordered regions is more complex as in these same X-ray structures; it is associated to the position of missing residues. Thus a continuum so seems to exist between rigidity, flexibility and disorder. However, it had not been precisely described. In this study, we used an ensemble of disordered proteins (or regions) and, we applied a structural alphabet to analyse their local conformation. This structural alphabet, namely Protein Blocks, had been efficiently used to highlight rigid local domains within flexible regions and so discriminates deformability and mobility concepts. Using an entropy index derived from this structural alphabet, we underlined its interest to measure these local dynamics, and to quantify, for the first time, continuum states from rigidity to flexibility and finally disorder. We also highlight non-disordered regions in the ensemble of disordered proteins in our study.

Published
2020

8. A structural entropy index to analyse local conformations in intrinsically disordered proteins

Author

Akhila, Melarkode Vattekatte, primary, Narwani, Tarun Jairaj, additional, Floch, Aline, additional, Maljković, Mirjana, additional, Bisoo, Soubika, additional, Shinada, Nicolas K., additional, Kranjc, Agata, additional, Gelly, Jean-Christophe, additional, Srinivasan, Narayanaswamy, additional, Mitić, Nenad, additional, and de Brevern, Alexandre G., additional

Published
2020
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9. Discrete analyses of protein dynamics

Author

Narwani, Tarun Jairaj, primary, Craveur, Pierrick, additional, Shinada, Nicolas K., additional, Floch, Aline, additional, Santuz, Hubert, additional, Vattekatte, Akhila Melarkode, additional, Srinivasan, Narayanaswamy, additional, Rebehmed, Joseph, additional, Gelly, Jean-Christophe, additional, Etchebest, Catherine, additional, and de Brevern, Alexandre G., additional

Published
2019
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10. Discrete analyses of protein dynamics.

Author

Narwani, Tarun Jairaj, Craveur, Pierrick, Shinada, Nicolas K., Floch, Aline, Santuz, Hubert, Vattekatte, Akhila Melarkode, Srinivasan, Narayanaswamy, Rebehmed, Joseph, Gelly, Jean-Christophe, Etchebest, Catherine, and de Brevern, Alexandre G.

Published
2020
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12. Data set of intrinsically disordered proteins analysed at a local protein conformation level.

Author

Melarkode Vattekatte A, Narwani TJ, Floch A, Maljković M, Bisoo S, Shinada NK, Kranjc A, Gelly JC, Srinivasan N, Mitić N, and de Brevern AG

Abstract

Intrinsic Disorder Proteins (IDPs) have become a hot topic since their characterisation in the 90s. The data presented in this article are related to our research entitled "A structural entropy index to analyse local conformations in Intrinsically Disordered Proteins" published in Journal of Structural Biology [1]. In this study, we quantified, for the first time, continuum from rigidity to flexibility and finally disorder. Non-disordered regions were also highlighted in the ensemble of disordered proteins. This work was done using the Protein Ensemble Database (PED), which is a useful database collecting series of protein structures considered as IDPs. The data set consists of a collection of cleaned protein files in classical pdb format that can be readily used as an input with most automatic analysis software. The accompanying data include the coding of all structural information in terms of a structural alphabet, namely Protein Blocks (PBs). An entropy index derived from PBs that allows apprehending the continuum between protein rigidity to flexibility to disorder is included, with information from secondary structure assignment, protein accessibility and prediction of disorder from the sequences. The data may be used for further structural bioinformatics studies of IDPs. It can also be used as a benchmark for evaluating disorder prediction methods., (© 2020 The Author(s).)

Published
2020
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13. In silico analysis of Glanzmann variants of Calf-1 domain of α IIb β 3 integrin revealed dynamic allosteric effect.

Author

Goguet M, Narwani TJ, Petermann R, Jallu V, and de Brevern AG

Subjects
Allosteric Regulation, Humans, Platelet Glycoprotein GPIIb-IIIa Complex genetics, Platelet Glycoprotein GPIIb-IIIa Complex metabolism, Allosteric Site, Molecular Dynamics Simulation, Mutation, Platelet Glycoprotein GPIIb-IIIa Complex chemistry, Thrombasthenia genetics
Abstract

Integrin α IIb β 3 mediates platelet aggregation and thrombus formation. In a rare hereditary bleeding disorder, Glanzmann thrombasthenia (GT), α IIb β 3 expression / function are impaired. The impact of deleterious missense mutations on the complex structure remains unclear. Long independent molecular dynamics (MD) simulations were performed for 7 GT variants and reference structure of the Calf-1 domain of α IIb . Simulations were analysed using a structural alphabet to describe local protein conformations. Common and flexible regions as well as deformable zones were observed in all the structures. The most flexible region of Calf-1 (with highest B-factor) is rather a rigid region encompassed into two deformable zones. Each mutated structure barely showed any modifications at the mutation sites while distant conformational changes were observed. These unexpected results question the relationship between molecular dynamics and allostery; and the role of these long-range effects in the impaired α IIb β 3 expression. This method is aimed at studying all α IIb β 3 sub-domains and impact of missense mutations at local and global structural level.

Published
2017
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