Research Publications
Welcome to our publications page. Here you can find a selection of our recent publications in the field of computational chemistry. Our lab specializes in molecular dynamics studies to explore protein folding, function, and hydration.
2023
81 Decoupling of Interactions between Model-Charged Peptides Reveals Key Factors Responsible for Liquid–Liquid Phase Separation. Debasis Saha and Biman Jana*. Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.3c03087
80 Preferential Ordering and Organization of Hydration Water Favor Nucleation of Ice by Ice-Nucleating Proteins over Antifreeze Proteins. Rahul Aich, Prasun Pal, Sandipan Chakraborty, and Biman Jana. Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.3c01641
79 Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control. Rabindranath Manna, José Onuchic*, Biman Jana*. PNAS. https://doi.org/10.1073/pnas.2215170120
78 Real-time Observation of Macroscopic Helical Morphologies under OM: A Curious Case of π-π Stacking Driven Molecular Self-assembly of an Organic Gelator Devoid of Hydrogen Bonding. Sourabh Bera, Sushmita Basu, Biman Jana*, Parthasarathi Dastidar*. Angewandte Chemie. https://doi.org/10.1002/ange.202216447
2022
77 Number of Hydrogen Bonds Per Unit Solvent Accessible Surface Area: A descriptor of funtional states of protein. Prasun Pal, Sandipan Chakraborty*, Biman Jana*. Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.2c05367
76 Molecular Factors of Ice Growth Inhibition for Hyperactive and Globular Antifreeze Proteins: Insights from Molecular Dynamics Simulation. Prasun Pal, Rahul Aich, Sandipan Chakraborty*, Biman Jana*. Langmuir. https://doi.org/10.1021/acs.langmuir.2c02149
75 Identifying the Template for Oligomer to Fibril Conversion for Amyloid‐β (1‐42) oligomers using Hamiltonian Replica Exchange Molecular Dynamics. Debasis Saha, Biman Jana* . ChemPhysChem. https://doi.org/10.1002/cphc.202200393
74 Direct Participation of Solvent Molecules in the Formation of Supramolecular Polymers. Goutam Ghosh, Anwesha Chakraborty, Prasun Pal, Biman Jana*, Suhrit Ghosh*. Chemistry A European Journal. https://doi.org/10.1002/chem.202201082
73 Curious Case of MAD2 Protein: Diverse Folding Intermediates Leading to Alternate Native States. Catherine Ghosh and Biman Jana*. Journal of Physical Chemistry B. 2022, 126, 9, 1904–1916
2021
72 Molecular Insight into the Effect of a Single-Nucleotide Polymorphic Variation on the Structure and Dynamics of Methionine Synthase Reductase and Its Association with Neural Tube Defects. Susanta Sadhukhan, Subhajit Maity, Sandipan Chakraborty, Silpita Paul, Dinesh Munian, Arup Kumar Pattanayak, Biman Jana*, and Madhusudan Das*. ACS Omega 2021, 6, 40, 26372–26380
71 Kinetic and Thermodynamic Stability Comparison for Fibrillar Form of Small Amyloid-β(1-42) Oligomers Using Scaled Molecular Dynamics. Debasis Saha, Biman Jana*. Physical chemistry chemical physics. 2021,23, 16897-16908
70 Differential Hydration of Ice-Binding Surface of Globular and Hyperactive Antifreeze Proteins. Prasun Pal, Sandipan Chakraborty*, Biman Jana*. Advanced Theory and Simulations, DOI- 10.1002/adts.202100090
69 Cold denaturation induced helix-to-helix transition and its implication to activity of helical antifreeze protein. Sridip Parui, Biman Jana*. Journal of Molecular Liquids, Volume 338, 15 September 2021, 116627
68 Role of Calcium in Modulating the Conformational Landscape and Peptide Binding Induced Closing of Calmodulin. Catherine Ghosh and Biman Jana*. Journal of Physical Chemistry B. 2021, 125, 9, 2317–2327
67 Mechanistic basis of propofol-induced disruption of kinesin processivity. Mandira Dutta, Susan P. Gilbert*, José N. Onuchic*, and Biman Jana*. Proceedings of the National Academy of Sciences 2021 118 (5) e2023659118
66 Computational modeling of dynein motor proteins at work. Mandira Dutta, Biman Jana*. Chemical Communications, 2021,57, 272-283
65 Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution. Ritaban Halder, Biman Jana*. Proteins: Structure, Function, and Bioinformatics, https://doi.org/10.1002/prot.25999
2020
64 On the Correlation between Pair Hydrophobicity and Mixing Enthalpies in Water-Alcohol Binary Mixtures. Ritaban Halder, Biman Jana* . Journal of Physical Chemistry B. 2020, 124, 37, 8023–8031
63 Structural insight into the effect of polymorphic variation on the functional dynamics of methionine synthase reductase: Implications in neural tube defects Susanta Sadhukhan, Subhajit Maity, Sandipan Chakraborty, Silpita Paul, Dinesh Munian, Arup Kumar Pattanayak, Biman Jana, Madhusudan Das* Chemical Biology and Drug Design (2020) https://doi.org/10.1111/cbdd.13780
62 Novel Mechanism of Cholesterol Transport by ABCA5 in Macrophages and Its Role in Dyslipidemia. Aleepta Guha Ray, Kamalika Roy Choudhury, Sandipan Chakraborty, Devasmita Chakravarty, Vivek Chander ,Biman Jana, Khawer N.Siddiqui, Arun Bandyopadhyay*. Journal of Molecular Biology (2020), 432, 17, 4922-4941
61 Deciphering the Role of the Non-ice-binding Surface in the Antifreeze Activity of Hyperactive Antifreeze Proteins.Prasun Pal, Sandipan Chakraborty*, and Biman Jana* J. Phys Chem B (2020) , 124, 23, 4686–4696
60 Intersubunit Assisted Folding of DNA Binding Domains in Dimeric Catabolite Activator Protein. Catherine Ghosh ,Biman Jana* J. Phys Chem B (2020) , 124, 8, 1411–1423
59 Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K+-ion across biological membranes. Manish Debnath, Sandipan Chakraborty, Y.Pavan Kumar, Ritapa Chaudhuri, Biman Jana, Jyotirmayee Dash* , Nature Communications ,volume11, Article number:469 (2020)
58 Mechanistic study of the ATP hydrolysis reaction in dynein motor protein. Rabindra Nath Manna, Mandira Dutta, Biman Jana.* Phys. Chem. Chem. Phys. (2020) 22, 1534-1542
2019
57 Role of AAA3 Domain in Allosteric Communication of Dynein Motor Proteins. Mandira Dutta, Biman Jana* ACS Omega (2019) 4, 26, 21921-21930
56 Exploring and Engineering the Conformational Landscape of Calmodulin through Specific Interactions. Ritaban Halder, Biman Jana* J. Phys Chem B (2019) 123, 44, 9321-9327
55 Relative Solvent Exposure of the Alpha-Helix and Beta-Sheet in Water Determines the Initial Stages of Urea and Guanidinium Chloride-Induced Denaturation of Alpha/Beta Proteins. Sridip Paruiand Biman Jana* J. Phys Chem B (2019) 123, 42, 8889-8900
54 Ordered hydration layer mediated ice adsorption of a globular antifreeze protein: A mechanistic insight, Sandipan Chakraborty and Biman Jana* Phys. Chem. Chem. Phys. (2019) 21, 19298-19310
53 Calcium Ion Implicitly Modulates the Adsorption Ability of Ion-Dependent Type II Antifreeze Proteins on Ice/Water Interface: A Structural Insight. Sandipan Chakraborty and Biman Jana* Metallomics (2019) 11, 1387-1400
52 Structural Insight and Ultrafast Dynamics of 2D-Porphyrin Nanostructures, Rajesh Bera, Sandipan Chakraborty, Sandip Kumar Nayak, Biman Jana, Amitava Patra* J. Phys Chem C (2019) 123, 25, 15815-15826
51 Molecular structure of a hyperactive antifreeze protein adsorbed to ice. Konrad Meister,C. J. Moll, Sandipan Chakraborty, Biman Jana, Arthur. L. DeVries, Hans Ramløv, and Huib J. Bakker. J. Chem. Phys. (2019) 150, 131101.
50 Solvent-Assisted Enhanced Emission of Cationic Perylene Diimide Supramolecular Assembly in Water: A Perspective from Experiment and Simulation. Kausik Bag, Ritaban Halder, Biman Jana,* Sudip Malik* J. Phys. Chem. C (2019) 123, 10, 6241-6249
49 Factors Promoting the Formation of Clathrate-like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure. Sridip Parui and Biman Jana* J. Phys. Chem. B (2019) DOI:10.1021/acs.jpcb.8b11172
48 Antifreeze proteins: An unusual tale of structural evolution, hydration and function. Sandipan Chakraborty and Biman Jana* Proceedings of the Indian National Academy of Sciences (2019) 85, 169-187
2018
47 Structural consequences of hereditary spastic paraplegia disease-related mutations in kinesin. Mandira Dutta, Michael R. Diehl, José N. Onuchic*, and Biman Jana* Proceedings of the National Academy of Sciences, USA (2018), DOI:https://doi.org/10.1073/pnas.1810622115
46 Molecular Insights into the Unusual Structure of an Antifreeze Protein with Hydrated Core. Sridip Parui, and Biman Jana* J. Phys. Chem. B (2018) DOI: 10.1021/acs.jpcb.8b05350
45 Unraveling the Crucial Role of Single Active Water Molecule in the Oxidative Cleavage of Aliphatic C-C bond of 2,4ʹ- dihydroxyacetophenone Catalyzed by DAD enzyme: A QM/MM Investigation. Rabindra Nath Manna, Tanmay Malakar, Biman Jana*, and Ankan Paul*. ACS Catalysis (2018) DOI: 10.1021/acscatal.8b03201
44 Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins. Qian Wang, Biman Jana, Michael R. Diehl, Margaret S. Cheung, Anatoly B. Kolomeisky, and José N. Onuchic*. Proceedings of the National Academy of Sciences, USA (2018) DOI: https://doi.org/10.1073/pnas.1806688115
43 Local environment of organic dyes in an ionic liquid-water mixture: FCS and MD simulation. Somen Nandi^, Sridip Parui^, Biman Jana* and Kankan Bhattacharyya*The Journal of Chemical Physics 149, 054501 (2018) (^:Equal contribution)
42 Unravelling the Composition Dependent Anomalies of Pair Hydrophobicity in Water-Ethanol Binary Mixtures. R. Halder and B. Jana. The Journal of Physical Chemistry B, 2018, 122 (26), pp 6801–6809
41 Optimum Number of Anchored Clathrate Water and Its Instantaneous Fluctuations Dictate Ice Plane Recognition Specificities of Insect Antifreeze Protein. S. Chakraborty and B. Jana* The Journal of Physical Chemistry B (2018) 122 (12), 3056–3067
40 Interaction of proteins with ionic liquid, alcohol and DMSO and in situ generation of gold nano-clusters in a cell. S. Nandi, S. Parui, R. Halder, B. Jana*, K. Bhattacharyya* Biophysical Reviews (2018) 10,757-768
2017
39 Molecular origin of the weak susceptibility of kinesin velocity to loads and its relation to the collective behavior of kinesins. Qian Wang, Michael R. Diehl, Biman Jana, Margaret S. Cheung, Anatoly B. Kolomeiskya, José N. Onuchic*, Proceedings of the National Academy of Sciences (2017), 114 (41) E8611-E8617.
38 Exciton Dynamics and Formation Mechanism of MEH-PPV Polymer -Based Nanostructures. A. G hosh, B. Jana, S. Chakraborty, S. Maiti, B. Jana, H.N. Ghosh, A. Patra*, The Journal of Physical Chemistry C (2017), 121 (38), 21062–21072.
37 Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules. S. Mondal^, S. Chaterjee^, R. Halder^, B. Jana*, P.C. Singh*, The Journal of Physical Chemistry B, (2017) 121 (32), 7681–7688 (^: equal contribution)
36 Pairwise Hydrophobicity at Low Temperature: Appearance of a Stable Second Solvent Separated Minimum with Possible Implication in Cold Denaturation. S. Parui, B. Jana*. The Journal of Physical Chemistry B, (2017) 121 (29), 7016–7026.
35 Molecular Insight into the Adsorption of Spruce budworm Antifreeze Protein to Ice Surface: A Clathrate Mediated Recognition Mechanism, S. Chakraborty, B. Jana*, Langmuir, 33 (28), 7202–7214 (2017)
34 Modulation of the Conformational Dynamics of Apo Adenylate Kinase through a π-cation Interaction. R. Halder, R. N. Manna, S. Chakraborty, B. Jana*, J. Phys. Chem. B, 121, 5699–5708 (2017)
33 Size and Structure of Cytochrome-c bound to Gold nano-clusters: Effect of Ethanol. C. Ghosh, Md. A. Amin, B. Jana, K. Bhattacharyya. Journal of Chemical Science. , Volume 129, Issue 7, pp 841–847.
32 Conformational and Hydration Properties Modulate the Ice Recognition by Type I Antifreeze Protein and its Mutants. S. Chakraborty, B. Jana. Phyiscal Chemistry Chemical Physics, 19, 11678-11689 (2017) (This article has been included in New Frontiers in Indian Research-themed collection published by RSC publishing)
2016
31 Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations, MA Amin, R Halder, C Ghosh, B Jana, K Bhattacharyya. The Journal of Chemical Physics, 145 (23), 235102, (2016)
30 Exploring the mechanochemical cycle of dynein motor proteins: structural evidence of crucial intermediates, Mandira Dutta, Biman Jana, Phys. Chem. Chem. Phys., 2016,18, 33085-33093.
29 Destabilization of Hydrophobic Core of Chicken Villin Headpiece in Guanidinium Chloride Induced Denaturation: Hint of π-Cation Interaction, S Parui, RN Manna, B JanaThe Journal of Physical Chemistry B 120 (36), 9599-9607, (2016).
28 Strain mediated adaptation is key for myosin mechanochemistry: Discovering general rules for motor activity, B Jana, JN Onuchic, PLoS Comput Biol 12 (8), e1005035, (2016).
27 Poly (ADP-ribose) polymers regulate DNA topoisomerase I (Top1) nuclear dynamics and camptothecin sensitivity in living cells, SK Das, I Rehman, A Ghosh, S Sengupta, P Majumdar, B Jana, BB Das Nucleic Acids Research, gkw665, (2016).
26 Solvent organization around the perfluoro group of coumarin 153 governs its photophysical properties: An experimental and simulation study of coumarin dyes in ethanol as well as fluorinated ethanol solvents, S Mondal, R Halder, B Biswas, B Jana, PC Singh, The Journal of chemical physics 144 (18), 184504, (2016).
25 Structural relaxation of acridine orange dimer in bulk water and inside a single live lung cell, R Chowdhury, S Nandi, R Halder, B Jana, K Bhattacharyya, The Journal of chemical physics 144 (6), 065101, (2016).
2015
24 Ionic liquid induced dehydration and domain closure in lysozyme: FCS and MD simulation, S Ghosh, S Parui, B Jana, K Bhattacharyya, he Journal of chemical physics 143 (12), 09B622_1, (2015).
23 Dimeric interactions and complex formation using direct coevolutionary couplings, RN Dos Santos, F Morcos, B Jana, AD Andricopulo, JN Onuchic, Scientific reports 5, 13652, (2015).
2014
22 From structure to function: the convergence of structure based models and co-evolutionary information, B Jana, F Morcos, JN Onuchic, Physical Chemistry Chemical Physics 16 (14), 6496-6507, (2014).
2013
21 Coevolutionary signals across protein lineages help capture multiple protein conformations, F Morcos, B Jana, T Hwa, JN Onuchic, Proceedings of the National Academy of Sciences 110 (51), 20533-20538, (2013).
20 Molecular Dynamics of Thermotropic Liquid Crystals: Anomalous relaxation dynamics of calamitic and discotic liquid crystals, B Jana, B Bagchi Journal of the Indian Institute of Science 89 (2), 75-86, (2012).
2012
19 The origin of minus-end directionality and mechanochemistry of Ncd motors, B Jana, C Hyeon, JN Onuchic, PLoS Comput Biol 8 (11), e1002783, (2012).
18 Dimethyl sulfoxide induced structural transformations and non -monotonic concentration dependence of conformational fluctuation around active site of lysozyme, S Roy, B Jana, B Bagchi, The Journal of chemical physics 136 (11), 03B608, (2012).
17 Hydration dynamics of protein molecules in aqueous solution: Unity among diversity, B Jana, S Pal, B Bagchi Journal of Chemical Sciences 124 (1), 317-325, (2012).
2011
16 Dynamic and thermodynamic anomalies of water at low temperatures: from bulk water to reverse micelles and DNA hydration layer, B Jana, RS Singh, R Biswas, B Bagchi, Current Science (Bangalore) 101 (7), 900-922, (2011).
15 Dynamic control of catalysis within biological cells, B Jana, B Bagchi,arXiv preprint arXiv:1105.5192, (2011).
14 Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase, B Jana, BV Adkar, R Biswas, B Bagchi, The Journal of chemical physics 134 (3), 01B617, (2011).
13 String-like propagation of the 5-coordinated defect state in supercooled water: molecular origin of dynamic and thermodynamic anomalies, B Jana, RS Singh, B Bagchi, Physical Chemistry Chemical Physics 13 (36), 16220-16226, (2011).
12 Theoretical and computational analysis of static and dynamic anomalies in water− DMSO binary mixture at low DMSO concentrations, S Roy, S Banerjee, N Biyani, B Jana, B Bagchi, The Journal of Physical Chemistry B 115 (4), 685-692, (2010).
11 Role of water in the enzymatic catalysis: study of ATP+ AMP→ 2ADP conversion by adenylate kinase, BV Adkar, B Jana, B Bagchi, The Journal of Physical Chemistry A 115 (16), 3691-3697, (2010).
2010
10 Enhanced tetrahedral ordering of water molecules in minor grooves of DNA: relative role of DNA rigidity, nanoconfinement, and surface specific interactions, B Jana, S Pal, B Bagchi, The Journal of Physical Chemistry B 114 (10), 3633-3638, (2010).
9 Solvation dynamics in dipolar liquids, B Bagchi, B Jana, Chemical Society Reviews 39 (6), 1936-1954, (2010).
2009
8 Dynamical transition of water in the grooves of DNA duplex at low temperature, D Biswal, B Jana, S Pal, B Bagchi, The Journal of Physical Chemistry B 113 (13), 4394-4399, (2009).
7 Intermittent dynamics, stochastic resonance and dynamical heterogeneity in supercooled liquid water, B Jana, B Bagchi, The Journal of Physical Chemistry B 113 (8), 2221-2224, (2009).
2008
6 Hydrogen bond breaking mechanism and water reorientational dynamics in the hydration layer of lysozyme, B Jana, S Pal, B Bagchi, The Journal of Physical Chemistry B 112 (30), 9112-9117 (2008).
2007
5 Orientational dynamics and energy landscape features of thermotropic liquid crystals: An analogy with supercooled liquids, B Jana, B Bagchi, Journal of Chemical Sciences 119 (5), 343-350, (2007).
4 Glassy orientational dynamics of rodlike molecules near the isotropic-nematic transition, B Jana, D Chakrabarti, B Bagchi, Physical Review E 76 (1), 011712, (2007).
3 Orientational relaxation in a discotic liquid crystal, D Chakrabarti, B Jana, B Bagchi, Physical Review E 75 (6), 061703, (2007).
2 Fiber optic sensing of liquid refractive index, A Banerjee, S Mukherjee, RK Verma, B Jana, TK Khan, M Chakroborty, ...Sensors and Actuators B: Chemical 123 (1), 594-605, (2007).
2006
1 Entropy of water in the hydration layer of major and minor grooves of DNA, B Jana, S Pal, PK Maiti, ST Lin, JT Hynes, B Bagchi, The Journal of Physical Chemistry B 110 (39), 19611-19618, (2006).