The Role of Nucleotide Opening Dynamics in Facilitated Target Search by DNA-Repair Proteins
Sujeet Kumar Mishra, Sangeeta, Dieter W. Heermann, Arnab Bhattacherjee*, BBA - Gene Regulatory Mechanisms, 2024 (DOI:10.1016/j.bbagrm.2024.195026).
Unusual weak and delayed GTPase activity of FtsZ from human pathogenic bacteria Helicobacter pylori
Sumiran Kumar Gurung, Sangeeta, Priyanka Dubey, Fatima Akhtar, Abhik Saha, Arnab Bhattacherjee*, Suman Kumar Dhar*. The Journal of Biochemistry, https://doi.org/10.1093/jb/mvad114, 2023.
How Do Nucleosome Dynamics Regulate Protein Search on DNA?
Sujeet Kumar Mishra & Arnab Bhattacherjee*. The Journal of Physical Chemistry B, 127(25):5702-5717, 2023.
Understanding the Target Search by Multiple Transcription Factors on Nucleosomal DNA
Sujeet Kumar Mishra & Arnab Bhattacherjee*. ChemPhysChem, 24(8):e202200644, 2023.
Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA
Sangeeta & Arnab Bhattacherjee*. PLoS ONE, 18(1):e0278396, 2023.
Understanding Protein Diffusion on Force Induced Stretched DNA Conformation
Anupam Mondal & Arnab Bhattacherjee*. Frontiers in Molecular Biosciences, 9:953689, 2022.
Nucleosome breathing facilitates cooperative binding of pluripotency transcription factors Sox2 and Oct4 to DNA
Anupam Mondal, Sujeet Kumar Mishra & Arnab Bhattacherjee*. Biophysical Journal, 121(23): 4526-4542, 2022.
Torsional behaviour of supercoiled DNA regulates recognition of architectural protein Fis on minicircle DNA
Anupam Mondal, Sangeeta & Arnab Bhattacherjee*. Nucleic Acids Research, 50(12): 6671-6686, 2022.
Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome
Sujeet Kumar Mishra, Kunhe Li, Simon Brauburger, Arnab Bhattacherjee, Nestor Norio Oiwa & Dieter W. Heermann*. Life, 12(4): 541, 2022
Kinetic origin of nucleosome invasion by pioneer transcription factors
Anupam Mondal, Sujeet Kumar Mishra & Arnab Bhattacherjee*. Biophysical Journal, 120(23):5219-5230, 2021
Mechanism of Dynamic Binding of Replication Protein A to ssDNA
Anupam Mondal & Arnab Bhattacherjee*. Journal of Chemical Information And Modeling, 60(10):5057-5069, 2020
BCG vaccination policy and preventive chloroquine usage: do they have an impact on COVID-19 pandemic?
Abhibhav Sharma, Saurabh Kumar Sharma, Yufang Shi, Enrico Bucci, Ernesto Carafoli, Gerry Melino, Arnab Bhattacherjee* & Gobardhan Das*. Cell Death & Disease, (11):516, 2020
Molecular dynamics simulations and biochemical characterization of Pf14-3-3 and PfCDPK1 interaction towards its role in growth of human malaria parasite
Ravi Jain, Pinki Dey, Sakshi Gupta, Soumya Pati, Arnab Bhattacherjee, Manoj Munde, & Shailja Singh. Biochemical Journal, 477(12):2153-2177, 2020.
Structural Basis of Enhanced Facilitated Diffusion of DNA Binding Proteins in Crowded Cellular Milieu
Pinki Dey & Arnab Bhattacherjee*. Biophysical Journal, 118(2):505-517, 2020
Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase
Pinki Dey & Arnab Bhattacherjee*. The Journal of Physical Chemistry B, 123(49):10354-10364, 2019.
Disparity in anomalous diffusion of proteins searching for their target DNA sites in a crowded medium is controlled by the size, shape and mobility of macromolecular crowders
Pinki Dey & Arnab Bhattacherjee*. Soft Matter, 15:1960-1969, 2019. The research is highlighted as Cover Page image of the journal.
Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins
Pinki Dey & Arnab Bhattacherjee*. Scientific Reports, 8:844, 2018.
Understanding the Role of DNA Topology in Target Search Dynamics of Proteins
Anupam Mondal & Arnab Bhattacherjee*. The Journal of Physical Chemistry B, 121:9372-9381, 2017.
Coarse-grained models for studying protein diffusion along DNA
Arnab Bhattacherjee*, Dana Krepel & Yaakov Levy*. WIREs Computational Molecular Science, 6:515-531, 2016.
Searching target sites on DNA by proteins: Role of DNA dynamics under confinement
Anupam Mondal & Arnab Bhattacherjee*. Nucleic Acid Research, 43:9176–9186, 2015.
Thermodynamic protein destabilization by GFP tagging: a case of inter-domain allostery
Miri Sokolovski, Arnab Bhattacherjee, Naama Kessler, (Yaakov) Koby Levy, & Amnon Horovitz. Biophysical Journal, 109(6):1157-1162, 2015.
Search by proteins for their DNA target site: 2. The effect of DNA conformation on the dynamics of multidomain proteins
Arnab Bhattacherjee & Yaakov Levy. Nucleic Acid Research, 42(20):12415-12424, 2014
Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding
Arnab Bhattacherjee & Yaakov Levy. Nucleic Acid Research, 42(20):12404-12414, 2014.
Conformational properties and aggregation of the 1- 93 fragment of apolipoprotein A-I
Jitka Petrlova, Arnab Bhattacherjee, Wouter Boomsma, Stefan Wallin, Jens Lagerstedt & Anders Irbäck. Protein Science, 23(11):1559-1571, 2014.
Hybrid Monte Carlo with Non-Uniform Step Size
Christian Holzgräfe & Arnab Bhattacherjee and Anders Irbäck. Journal of Chemical Physics, 140(4):044105, 2014.
Exploring protein-peptide binding specificity through computational peptide screening
Arnab Bhattacherjee & Stefan Wallin. Plos Computational Biology, 9(10):e1003277, 2013.
Coupled Folding-Binding in a Hydrophobic/Polar Protein Model: Impact of Synergistic Folding and Disordered Flanks
Arnab Bhattacherjee & Stefan Wallin. Biophysical Journal, 102(3):569-578, 2012.
Role of Conformational Heterogeniety on Protein Misfolding
Anupaul Baruah, Arnab Bhattacherjee & Parbati Biswas. Soft Matter, 8(16):4432-4440, 2012.
Designing MisFolded Protein Sequences by Energy Landscaping
Arnab Bhattacherjee & Parbati Biswas. Journal of Physical Chemistry B, 115(1):113-119, 2011.
Role of Foldability and Stability in Designing Real Protein Sequences
Arnab Bhattacherjee & Parbati Biswas. Physical Chemistry Chemical Physics, 13(20):9223-9231, 2011. Selected in the list of Top 20 Articles,in the Domain of Article 21468433, Since its Publication (2011)
Neutrality and Evolvability of Designed Protein Sequences
Arnab Bhattacherjee & Parbati Biswas. Physical Review E, 82:011906, 2010. Also selected for 15th July 2010 issue of Virtual Journal of Biological Physics Research
Statistical Theory of Neutral Protein Evolution by Random Site Mutations
Arnab Bhattacherjee & Parbati Biswas. Journal of Chemical Sciences, 121(5):887-896, 2009.
Combinatorial Design of Protein Sequences with Application to Lattice and Real Proteins
Arnab Bhattacherjee and Parbati Biswas. Journal of Chemical Physics, 131(12):125101, 2009. Also selected for 1st October 2009 issue of Virtual Journal of Biological Physics Research.
Statistical Theory of Protein Sequence Design by Random Mutation
Arnab Bhattacherjee and Parbati Biswas. Journal of Physical Chemistry B, 113(16):5520-5527, 2009.