Publications

Submitted papers

• (2024) Krishnakanth Baratam and Anand Srivastava*, "SOP-MULTI: A self-organized polymer based coarse-grained model for multi-domain and intrinsically disordered proteins with conformation ensemble consistent with experimental scattering data (submitted)", bioRxiv link: https://doi.org/10.1101/2024.04.29.591764

• (2024) Chandramouli Natarajan and Anand Srivastava*, " Efficiently determining membrane-bound conformations of peripheral membrane proteins using replica exchange with hybrid tempering, submitted", bioRxiv link: https://doi.org/10.1101/2024.05.04.592548  

• (2024) Sahithya Iyer and Anand Srivastava*, "Membrane lateral organization from potential energy disconnectivity graph", Review article, Biophysical Chemistry, Special Issue on Biomolecular Energy Landscapes (Submitted)

• (2024) Madhusmita Tripathy* and Anand Srivastava*, "Non-affine deformation analysis and 3D packing defects: A new way to probe membrane heterogeneity in molecular simulations", Invited contribution to Methods in Enzymology book series (Biophysical Approaches for the Study of Membrane Structure), Editors: Tobais Baumgart and Markus Deserno) In Press: https://authors.elsevier.com/a/1j2qfHRzCT-Y%7E

• (2024) Irawati Roy, Sangeetha Balasubramanian, Rajeswari Appadurai* and Anand Srivastava*, "Atomic-scale structural insights into the functional roles of the full low complexity domain of the hnRNPA1 protein", bioRxiv link: https://www.biorxiv.org/content/10.1101/2023.08.21.554222v1

Published

• (2024) Poonam Pandey and Anand Srivastava*, "sAMP-VGG16: Drude polarizable force-field assisted image-based deep neural network prediction model for short antimicrobial peptides", PROTEINS: Structure, Function, and Bioinformatics, https://onlinelibrary.wiley.com/doi/10.1002/prot.26681 

• (2024) Rajlaxmi Saha, Prathyush Poduval, Krishnakanth Baratam, Jayashree Nagesh, Anand Srivastava*, “Membrane catalysed formation of nucleotide clusters and its role in the origins of life”, JPCB, https://pubs.acs.org/doi/10.1021/acs.jpcb.3c08061

• (2023) Harini SureshKumar, Rajeswari Appadurai and Anand Srivastava*, "Glycans modulate lipid binding in Lili-Mip lipocalin protein", Glycobiology Journal, https://doi.org/10.1093/glycob/cwad094

• (2023) Sangeetha Balasubramanian, Shovamayee Maharana, and Anand Srivastava*, “Boundary residues” between the folded RNA recognition motif and disordered RGG domains are critical for FUS–RNA binding" , Journal of Biological Chemistry, https://doi.org/10.1016/j.jbc.2023.105392 (In Press,)

• (2023) Rajeswari Appadurai, Jaya Krishna, Massimiliano Bonomi, Paul Robustelli* and Anand Srivastava*, "Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding" Journal of Chemical Theory And Computation, https://doi.org/10.1021/acs.jctc.3c00224

• (2023) Madhusmita Tripathy* and Anand Srivastava*, "Lipid packing in biological membranes governs protein localization and membrane permeability", Biophysical Journal, https://doi.org/10.1016/j.bpj.2023.05.028 

• (2023) Himani Khurana, Krishnakanth Baratam, Soumya Bhattacharyya, Anand Srivastava, Thomas J Pucadyil*, "Mechanistic analysis of a novel membrane-interacting variable loop in the pleckstrin-homology domain critical for dynamin function." PNAS, https://doi.org/10.1073/pnas.2215250120

• (2022) Tripathy, M., Srivastava, A., Sastry, and Madan Rao*, "Protein as evolvable functionally constrained amorphous matter". Journal of Biosciences . https://doi.org/10.1007/s12038-022-00313-3

• (2022) Kumar, G., Duggisetty, S.C. & Srivastava, A. A Review of Mechanics-Based Mesoscopic Membrane Remodeling Methods: Capturing Both the Physics and the Chemical Diversity. J Membrane Biol (2022). https://doi.org/10.1007/s00232-022-00268-4

• (2022) Gaurav Kumar and Anand Srivastava,"Membrane Remodeling Due to a Mixture of Multiple Types of Curvature Proteins",J. Chem. Theory Comput. 2022, 18, 9, 5659–5671(2022) https://doi.org/10.1021/acs.jctc.2c00126

• (2022) Akshara Sharma, Aniruddha Seal, Sahithya S. Iyer, and Anand Srivastava,"Enthalpic and entropic contributions to interleaflet coupling drive domain registration and antiregistration in biological membrane",Phys. Rev. E 105, 044408 (2022) https://doi.org/10.1103/PhysRevE.105.044408

• (2022) Prakash Kulkarni, Vitor B. P. Leite, Susmita Roy, Supriyo Bhattacharyya, Atish Mohanty, Srisairam Achuthan, Divyoj Singh, Rajeswari Appadurai, Govindan Rangarajan, Keith Weninger, John Orban, Anand Srivastava, Mohit Kumar Jolly, Jose N. Onuchic, Vladimir N. Uversky, and Ravi Salgia , "Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma", Biophysics Rev. 3, 011306 (2022) https://doi.org/10.1063/5.0080512

• (2021) K. Baratam, K. Jha and A. Srivastava*, “Flexible pivoting of dynamin PH-domain catalyzes fission: Insights into molecular degrees of freedom”, Molecular Biology of the Cell (2021) https://doi.org/10.1091/mbc.E20-12-0794

• (2021) A. Rajeswari, J. Nagesh and A. Srivastava*, “High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme”, Nature Communications (2021) https://doi.org/10.1038/s41467-021-21105-7 

• (2021) D. Mishra, S. Pahujani, N. Mitra, A. Srivastava*, R. Srinivasan*, “Identification of a Potential Membrane-Targeting Sequence in the C-Terminus of the F Plasmid Segregation Protein SopA”, Journal of Membrane Biology (2021) https://doi.org/10.1007/s00232-020-00157-8 

• (2021) Gorai, B., Sahoo, A. K., Srivastava, A., Dixit, N. M., and Maiti, P. K.*, & "Concerted Interactions between Multiple gp41 Trimers and the Target Cell Lipidome  May Be Required for HIV-1 Entry", J . Chem. Inf. Model. &  61, & 444–454. https://doi.org/10.1021/acs.jcim.0c01291

• (2020) M. Tripathy, T. Subasini and A. Srivastava*, “Three-Dimensional Packing Defects in Lipid Membrane as a Function of Membrane Order” – Journal of Chemical Theory and Computation (2020) https://doi.org/10.1021/acs.jctc.0c00609 

• (2020) S. Iyer and A. Srivastava*, “Degeneracy in molecular scale organization of biological membranes”, Soft Matter (2020) https://doi.org/10.1039/D0SM00619J 

• (2020) J. Bodosa, S. Iyer and A. Srivastava*, “Preferential protein partitioning in biological membrane with coexisting liquid ordered and liquid disordered phase behaviour: Underlying design principles” –Journal of Membrane Biology (2020) [Review paper] https://doi.org/10.1007/s00232-020-00150-1 

• (2020) Interpretation of Phase Boundary Fluctuation Spectra in Biological Membranes with Nanoscale Organization”, Journal of Chemical Theory and Computation (2019) https://doi.org/10.1021/acs.jctc.9b00929 

• (2019) R. Appadurai, V. Uversky and A. Srivastava*, “The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane  Proteins”, The Journal of Membrane Biology (2019) [Review paper] http://doi.org/10.1007/s00232-019-00069-2 

• (2018) S. S. Iyer, M. Tripathy and A. Srivastava*,“Liquid-liquid Phase Coexistence in Biological Membrane: Insights from Local Nonaffine Deformation of Lipids”, Biophysical Journal (2018) https://doi.org/10.1016/j.bpj.2018.05.021 

• (2018) M. Tripathy, S. S. Iyer and A. Srivastava*, “Molecular Origin of Spatiotemporal Heterogeneity in Biomembranes With Coexisting Liquid Phases: Insights From Topological Rearrangements and Lipid Packing Defects”, Advances in Biomembranes and Lipid Self-Assembly – Vol 28 (2018) [Book Chapter] https://doi.org/10.1016/bs.abl.2018.06.001 

• (2018) S. Mathesan, M. Tripathy, A. Srivastava* and P. Ghosh*, “Non-Affine Deformation of Free Volume during Strain Dependent Diffusion in Polymer Thin Films” Polymer (2018) https://doi.org/10.1016/j.polymer.2018.09.035 

• (2018) R. Deo, M. S. Kushwah, S. C. Karmerkar, N. Y. Kadam, S. Dar1, K. Babu, A. Srivastava and T. J. Pucadyil*, “ATP-dependent membrane remodeling links EHD1 functions to endocytic recycling” Nature Communication (2018) https://www.nature.com/articles/s41467-018-07586-z 

• (2017) C. Kotyada, A. Maulik, A. Srivastava, A. and M. Singh* “Mechanistic Insights into the Differential Catalysis by RheB and Its Mutants: Y35A and Y35A-D65A”, ACS Omega (2017) https://doi.org/10.1021/acsomega.7b01025 

• (2017) A.J Pak, J.M.A Grime, P. Sengupta, P., A.K. Chen, A.E.P. Durumeric, A. Srivastava, M. Yeager, J.A.G. Briggs, J. Lippincott-Schwartz*, and G.A. Voth*, “Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane”, PNAS (2017) https://doi.org/10.1073/pnas.1706600114