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  1. Article ; Online: Fundamentals of Electrophoresis 2024.

    Dutta, Prashanta / Gaš, Bohuslav

    Electrophoresis

    2024  Volume 45, Issue 7-8, Page(s) 587–588

    MeSH term(s) Electrophoresis/methods ; Humans ; Periodicals as Topic
    Language English
    Publishing date 2024-04-26
    Publishing country Germany
    Document type Editorial ; Introductory Journal Article
    ZDB-ID 619001-7
    ISSN 1522-2683 ; 0173-0835
    ISSN (online) 1522-2683
    ISSN 0173-0835
    DOI 10.1002/elps.202470044
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  2. Article ; Online: Editorial.

    Dutta, Prashanta / Gaš, Bohuslav

    Electrophoresis

    2023  Volume 44, Issue 7-8, Page(s) 633

    Language English
    Publishing date 2023-04-17
    Publishing country Germany
    Document type Editorial
    ZDB-ID 619001-7
    ISSN 1522-2683 ; 0173-0835
    ISSN (online) 1522-2683
    ISSN 0173-0835
    DOI 10.1002/elps.202370044
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  3. Article ; Online: Enhanced Sampling for Conformational Changes and Molecular Mechanisms of Human NTHL1.

    Odstrcil, Ryan E / Dutta, Prashanta / Liu, Jin

    The journal of physical chemistry letters

    2024  Volume 15, Issue 11, Page(s) 3206–3213

    Abstract: The functionalities of proteins rely on protein conformational changes during many processes. Identification of the protein conformations and capturing transitions among different conformations are important but extremely challenging in both experiments ... ...

    Abstract The functionalities of proteins rely on protein conformational changes during many processes. Identification of the protein conformations and capturing transitions among different conformations are important but extremely challenging in both experiments and simulations. In this work, we develop a machine learning based approach to identify a reaction coordinate that accelerates the exploration of protein conformational changes in molecular simulations. We implement our approach to study the conformational changes of human NTHL1 during DNA repair. Our results identified three distinct conformations: open (stable), closed (unstable), and bundle (stable). The existence of the bundle conformation can rationalize recent experimental observations. Comparison with an NTHL1 mutant demonstrates that a closely packed cluster of positively charged residues in the linker could be a factor to search when screening for genetic abnormalities. Results will lead to a better modulation of the DNA repair pathway to protect against carcinogenesis.
    MeSH term(s) Humans ; Proteins/chemistry ; Protein Conformation ; Molecular Dynamics Simulation ; Deoxyribonuclease (Pyrimidine Dimer)
    Chemical Substances Proteins ; NTHL1 protein, human (EC 3.1.25.1) ; Deoxyribonuclease (Pyrimidine Dimer) (EC 3.1.25.1)
    Language English
    Publishing date 2024-03-14
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.4c00161
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  4. Article ; Online: Fundamentals of Electrophoresis 2018.

    Dutta, Prashanta

    Electrophoresis

    2018  Volume 39, Issue 5-6, Page(s) 689

    MeSH term(s) Biosensing Techniques/instrumentation ; Biosensing Techniques/methods ; Cell Adhesion ; Electromagnetic Fields ; Electrophoresis/methods ; Microfluidics/instrumentation ; Microfluidics/methods ; Models, Theoretical ; Surface Properties
    Language English
    Publishing date 2018-03-01
    Publishing country Germany
    Document type Editorial ; Introductory Journal Article
    ZDB-ID 619001-7
    ISSN 1522-2683 ; 0173-0835
    ISSN (online) 1522-2683
    ISSN 0173-0835
    DOI 10.1002/elps.201870044
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  5. Article ; Online: Fundamentals of Electrophoresis 2022.

    Gaš, Bohuslav / Dutta, Prashanta

    Electrophoresis

    2022  Volume 43, Issue 5-6, Page(s) 655

    MeSH term(s) Electrophoresis/methods
    Language English
    Publishing date 2022-03-14
    Publishing country Germany
    Document type Editorial ; Introductory Journal Article
    ZDB-ID 619001-7
    ISSN 1522-2683 ; 0173-0835
    ISSN (online) 1522-2683
    ISSN 0173-0835
    DOI 10.1002/elps.202270035
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  6. Article ; Online: Prediction of the Peptide-TIM3 Binding Site in Inhibiting TIM3-Galectin 9 Binding Pathways.

    Odstrcil, Ryan E / Dutta, Prashanta / Liu, Jin

    Journal of chemical theory and computation

    2023  Volume 19, Issue 18, Page(s) 6500–6509

    Abstract: T-cell immunoglobulin and mucin domain-containing protein-3 (TIM3) is an important receptor protein that modulates the immune system. The binding of TIM3 with Galectin 9 (GAL9) triggers immune system suppression, but the TIM3-GAL9 binding can be ... ...

    Abstract T-cell immunoglobulin and mucin domain-containing protein-3 (TIM3) is an important receptor protein that modulates the immune system. The binding of TIM3 with Galectin 9 (GAL9) triggers immune system suppression, but the TIM3-GAL9 binding can be inhibited by binding of the peptide P26 to TIM3. A fast and accurate prediction of the P26-TIM3 binding site is crucial and a prerequisite for the investigation of P26-TIM3 interactions and TIM3-GAL9 binding pathways. Here, we present a machine learning approach, which considers protein conformational changes, to quickly identify the ligand-binding site on TIM3. Our results show that the P26 binding site is located near the C″-D loop of TIM3. Further simulations show that the binding pose is stabilized by a variety of electrostatic and hydrophobic interactions. Binding of P26 can alter the conformations of nearby glycan side chains on TIM3, providing possible mechanisms of how P26 inhibits TIM3-GAL9 binding pathways. The insights from this work will facilitate the identification of other peptides or antibodies that may also inhibit the TIM3-GAL9 pathways and eventually lead to improved attempts in the modulation of the TIM3-GAL9 immunosuppression pathways. The strategies and machine learning method can be generalized to study ligand-receptor binding when the conformational changes during the binding are important.
    MeSH term(s) Hepatitis A Virus Cellular Receptor 2/metabolism ; Ligands ; Binding Sites ; Galectins/metabolism ; Peptides
    Chemical Substances Hepatitis A Virus Cellular Receptor 2 ; Ligands ; Galectins ; Peptides
    Language English
    Publishing date 2023-08-30
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.3c00487
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  7. Article ; Online: Editorial Fundamentals 2021.

    Dutta, Prashanta / Gaš, Bohuslav

    Electrophoresis

    2021  Volume 42, Issue 7-8, Page(s) 813

    MeSH term(s) Editorial Policies
    Language English
    Publishing date 2021-04-17
    Publishing country Germany
    Document type Editorial ; Introductory Journal Article
    ZDB-ID 619001-7
    ISSN 1522-2683 ; 0173-0835
    ISSN (online) 1522-2683
    ISSN 0173-0835
    DOI 10.1002/elps.202170072
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  8. Article ; Online: Effects of receptor properties on particle internalization through receptor-mediated endocytosis.

    Billah, Md Muhtasim / Deng, Hua / Dutta, Prashanta / Liu, Jin

    Soft matter

    2023  Volume 19, Issue 31, Page(s) 5907–5915

    Abstract: Receptor-mediated endocytosis (RME) is a highly complex process carried out by bioparticles, such as viruses and drug carriers, to enter cells. The discovery of both clathrin-dependent and clathrin-free pathways makes the RME process even more intriguing. ...

    Abstract Receptor-mediated endocytosis (RME) is a highly complex process carried out by bioparticles, such as viruses and drug carriers, to enter cells. The discovery of both clathrin-dependent and clathrin-free pathways makes the RME process even more intriguing. Numerical models have been developed to facilitate the exploration of the process. However, the impacts of the receptor properties on RME have been less studied partially due to the oversimplifications of the receptor models. In this paper, we implement a stochastic model to systematically investigate the effects of mechanical (receptor flexure), geometrical (receptor length) and biochemical (ligand-receptor cutoff) properties of receptors, on RME with and without the existence of clathrin. Our simulation results show that the receptor's flexural rigidity plays an important role in RME with clathrin. There is a threshold beyond which particle internalization will not occur. Without clathrin, it is very difficult to achieve complete endocytosis with ligand-receptor interactions alone. A shorter receptor length and longer ligand-receptor reaction cutoff promote the formation of ligand-receptor bonds and facilitate particle internalization. Complete internalization can only be obtained with an extremely short receptor length and long reaction cutoff. Therefore, there are most likely some additional mechanisms to drive the membrane deformation in clathrin-free RME. Our results yield important fundamental insights into RME and provide crucial guidance when correlating the simulation results with experimental observations.
    MeSH term(s) Ligands ; Endocytosis ; Clathrin/metabolism
    Chemical Substances Ligands ; Clathrin
    Language English
    Publishing date 2023-08-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/d3sm00149k
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  9. Article ; Online: LINES: Log-Probability Estimation via Invertible Neural Networks for Enhanced Sampling.

    Odstrcil, Ryan E / Dutta, Prashanta / Liu, Jin

    Journal of chemical theory and computation

    2022  Volume 18, Issue 10, Page(s) 6297–6309

    Abstract: It is very challenging to sample a molecular process with large activation energies using molecular dynamics simulations. Current enhanced sampling methodologies, such as umbrella sampling and metadynamics, rely on the identification of appropriate ... ...

    Abstract It is very challenging to sample a molecular process with large activation energies using molecular dynamics simulations. Current enhanced sampling methodologies, such as umbrella sampling and metadynamics, rely on the identification of appropriate reaction coordinates for a system. In this paper, we developed a method for log-probability estimation via invertible neural networks for enhanced sampling (LINES). This iterative scheme utilizes a normalizing flow machine learning model to learn the underlying free energy surface (FES) of a system as a function of molecular coordinates and then applies a gradient-based optimization method to the learned normalizing flow to identify reaction coordinates. A biasing potential is then evaluated over a tabulated grid of the reaction coordinate values, which can be applied to the next round of simulations for enhanced sampling, resulting in more efficient sampling. We tested the accuracy and efficiency of the LINES method in sampling the FES using the alanine dipeptide system. We also demonstrated the effectiveness of identification of reaction coordinates through simulation of cyclobutanol unbinding from β-cyclodextrin and the folding/unfolding of CLN025─a variant of the peptide Chignolin. The LINES method can be extended to the study of large-scale protein systems with complex nonlinear reaction pathways.
    MeSH term(s) Alanine/chemistry ; Dipeptides/chemistry ; Molecular Dynamics Simulation ; Neural Networks, Computer ; Peptides ; Probability ; beta-Cyclodextrins
    Chemical Substances Dipeptides ; Peptides ; beta-Cyclodextrins ; Alanine (OF5P57N2ZX)
    Language English
    Publishing date 2022-09-13
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.2c00254
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  10. Article ; Online: Effect of Slp4-a on Membrane Bending During Prefusion of Vesicles in Blood-Brain Barrier.

    Van Dinh, Quyen / Liu, Jin / Dutta, Prashanta

    Journal of biomechanical engineering

    2022  Volume 145, Issue 1

    Abstract: Vesicle exocytosis is a promising pathway for brain drug delivery through the blood-brain barrier to treat neurodegenerative diseases. In vesicle exocytosis, the membrane fusion process is initiated by the calcium sensor protein named synaptotagmin-like ... ...

    Abstract Vesicle exocytosis is a promising pathway for brain drug delivery through the blood-brain barrier to treat neurodegenerative diseases. In vesicle exocytosis, the membrane fusion process is initiated by the calcium sensor protein named synaptotagmin-like protein4-a (Slp4-a). Understanding conformational changes of Slp4-a during the prefusion stage of exocytosis will help to develop vesicle-based drug delivery to the brain. In this work, we use molecular dynamics (MD) simulations with a hybrid force field coupling united-atom protein model with MARTINI coarse-grained (CG) solvent to capture the conformational changes of Slp4-a during the prefusion stage. These hybrid coarse-grained simulations are more efficient than all-atom MD simulations and can capture protein interactions and conformational changes. Our simulation results show that the calcium ions play critical roles during the prefusion stage. Only one calcium ion can remain in each calcium-binding pocket of Slp4-a C2 domains. The C2B domain of calcium-unbound Slp4-a remains parallel to the endothelial membrane, while the C2B domain of calcium-bound Slp4-a rotates perpendicular to the endothelial membrane to approach the vesicular membrane. For the calcium-bound case, three Slp4-a proteins can effectively bend lipid membranes at the prefusion stage, which could later trigger lipid stalk between membranes. This work provides a better understanding how C2 domains of Slp4-a operate during vesicle exocytosis from an endothelial cell.
    MeSH term(s) Blood-Brain Barrier/metabolism ; Calcium/metabolism ; Exocytosis ; Lipids ; Membrane Fusion
    Chemical Substances Lipids ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2022-07-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 243094-0
    ISSN 1528-8951 ; 0148-0731
    ISSN (online) 1528-8951
    ISSN 0148-0731
    DOI 10.1115/1.4054985
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