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Article ; Online: Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods.

Sarkar, Raju / Mainan, Avijit / Roy, Susmita

Chemical communications (Cambridge, England)

2024 Volume 60, Issue 27, Page(s) 3624–3644

Abstract: RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge ... ...

Abstract	RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg
MeSH term(s)	RNA/chemistry ; Water/chemistry ; Computer Simulation ; Metals
Chemical Substances	RNA (63231-63-0) ; Water (059QF0KO0R) ; Metals
Language	English
Publishing date	2024-03-28
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d3cc06105a
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: In vitro

Jo, Yongdeok / Sarkar, Naboneeta / Bose, Susmita

Journal of materials chemistry. B

2023 Volume 11, Issue 24, Page(s) 5503–5513

Abstract: Three-dimensional printed (3DP) tricalcium phosphate (TCP) scaffolds can guide bone regeneration, especially for patient-specific defect repair applications in low-load bearing sites. Epigallocatechin gallate (EGCG), a green tea compound, has gained ... ...

Abstract	Three-dimensional printed (3DP) tricalcium phosphate (TCP) scaffolds can guide bone regeneration, especially for patient-specific defect repair applications in low-load bearing sites. Epigallocatechin gallate (EGCG), a green tea compound, has gained attention as a safer alternative treatment for bone disorders. The 3DP TCP scaffold is designed for localized EGCG delivery, which can enhance
MeSH term(s)	Humans ; Osteogenesis ; Bone and Bones ; Calcium Phosphates/pharmacology ; Human Umbilical Vein Endothelial Cells
Chemical Substances	epigallocatechin gallate (BQM438CTEL) ; calcium phosphate (97Z1WI3NDX) ; tricalcium phosphate (K4C08XP666) ; Calcium Phosphates
Language	English
Publishing date	2023-06-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2702241-9
ISSN	2050-7518 ; 2050-750X
ISSN (online)	2050-7518
ISSN	2050-750X
DOI	10.1039/d2tb02210a
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Article ; Online: A Halogen-Bond-Driven Artificial Chloride-Selective Channel Constructed from 5-Iodoisophthalamide-based Molecules.

Sharma, Rashmi / Sarkar, Susmita / Chattopadhayay, Sandip / Mondal, Jagannath / Talukdar, Pinaki

Angewandte Chemie (International ed. in English)

2024 Volume 63, Issue 19, Page(s) e202319919

Abstract: Despite considerable emphasis on advancing artificial ion channels, progress is constrained by the limited availability of small molecules with the necessary attributes of self-assembly and ion selectivity. In this study, a library of small molecules ... ...

Abstract	Despite considerable emphasis on advancing artificial ion channels, progress is constrained by the limited availability of small molecules with the necessary attributes of self-assembly and ion selectivity. In this study, a library of small molecules based on 5-haloisophthalamide and a non-halogenated isophthalamide were examined for their ion transport properties across the lipid bilayer membranes, and the finding demonstrates that the di-hexyl-substituted 5-iodoisophthalamide derivative exhibits the highest level of activity. Furthermore, it was established that the highest active compound facilitates the selective chloride transport that occurs via an antiport-mediated mechanism. The crystal structure of the compound unveils a distinctive self-assembly of molecules, forming a zig-zag channel pore that is well-suited for the permeation of anions. Planar bilayer conductance measurements proved the formation of chloride selective channels. A molecular dynamics simulation study, relying on the self-assembled component derived from the crystal structure, affirmed the paramount significance of intermolecular hydrogen bonding in the formation of supramolecular barrel-rosette structures that span the bilayer. Furthermore, it was demonstrated that the transport of chloride across the lipid bilayer membrane is facilitated by the synergistic effects of halogen bonding and hydrogen bonding within the channel.
Language	English
Publishing date	2024-04-04
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202319919
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Article ; Online: A Synergistic View on Osmolyte's Role against Salt and Cold Stress in Biointerfaces.

Sarkar, Susmita / Narayanan, Tharangattu N / Mondal, Jagannath

Langmuir : the ACS journal of surfaces and colloids

2023 Volume 39, Issue 49, Page(s) 17581–17592

Abstract: We present our perspective on the role of osmolytes in mitigating abiotic stresses such as hypersalinity and sudden temperature changes. While the stabilizing effect of osmolytes on protein tertiary structures has been extensively studied, their direct ... ...

Abstract	We present our perspective on the role of osmolytes in mitigating abiotic stresses such as hypersalinity and sudden temperature changes. While the stabilizing effect of osmolytes on protein tertiary structures has been extensively studied, their direct impact on abiotic stress factors has eluded mainstream attention. Via highlighting a set of recent success stories of a joint venture of computer simulations and experimental measurements, we summarize the mechanistic insights into osmolytic action, particularly in the context of salt stress and combined cold-salt stress at the interface of biomolecular surfaces and saline environments. We stress the importance of chemical specificity in osmolytic activity, the interplay of differential osmolytic behaviors against heterogeneous salt stress, and the capability of osmolytes to adopt combined actions. Additionally, we discuss the potential of incorporating nanomaterial-based systems to enrich our understanding of osmolyte bioactions and facilitate their practical applications. We anticipate that this discourse will inspire interdisciplinary collaborations and motivate further investigations on osmolytes, ultimately broadening their applications in the fields of health and disease.
MeSH term(s)	Cold-Shock Response ; Proteins/chemistry ; Cold Temperature
Chemical Substances	Proteins
Language	English
Publishing date	2023-12-03
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.3c02397
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Article ; Online: Mechanistic Insights on ATP's Role as a Hydrotrope.

Sarkar, Susmita / Mondal, Jagannath

The journal of physical chemistry. B

2021 Volume 125, Issue 28, Page(s) 7717–7731

Abstract: Hydrotropes are the small amphiphilic molecules which help in solubilizing hydrophobic entities in an aqueous medium. Recent experimental investigation has provided convincing evidence that adenosine triphosphate (ATP), besides being ... ...

Abstract	Hydrotropes are the small amphiphilic molecules which help in solubilizing hydrophobic entities in an aqueous medium. Recent experimental investigation has provided convincing evidence that adenosine triphosphate (ATP), besides being the
MeSH term(s)	Adenosine Triphosphate ; Hydrophobic and Hydrophilic Interactions ; Ions ; Polymers ; Water
Chemical Substances	Ions ; Polymers ; Water (059QF0KO0R) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2021-07-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c03964
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Article ; Online: Micelle encapsulated curcumin and piperine-laden 3D printed calcium phosphate scaffolds enhance in vitro biological properties.

Bose, Susmita / Sarkar, Naboneeta / Majumdar, Ujjayan

Colloids and surfaces. B, Biointerfaces

2023 Volume 231, Page(s) 113563

Abstract: Limitations in the current clinical management of critical-sized osseous defects have driven the need for multifunctional bone constructs. The ideal bone scaffold should possess advanced microarchitecture, well-defined pore interconnectivity, and supply ... ...

Abstract	Limitations in the current clinical management of critical-sized osseous defects have driven the need for multifunctional bone constructs. The ideal bone scaffold should possess advanced microarchitecture, well-defined pore interconnectivity, and supply biological signals, which actively guide and control tissue regeneration while simultaneously preventing post-implantation complications. Here, a natural medicine-based localized drug delivery from 3D printed scaffold is presented, which offers controlled release of curcumin, piperine from nano-sized polymeric micelles, and burst release of antibacterial carvacrol from the coating endowing the scaffold with their distinct, individual biological properties. This functionalized scaffold exhibits improved osteoblast (hFOB) cell attachment, 4-folds higher hFOB proliferation, and 73% increased hFOB differentiation while simultaneously providing cytotoxicity towards osteosarcoma cells with 61% lesser viability compared to control. In vitro, early tube formation (p < 0.001) indicates that the scaffolds can modulate the endothelial cellular network, critical for faster wound healing. The scaffold also exhibits 94% enhanced antibacterial efficacy (p < 0.001) against gram-positive Staphylococcus aureus, the main causative bacteria for osteomyelitis. Together, the multifunctional scaffolds provide controlled delivery of natural biomolecules from the nano-sized micelle-loaded 3D printed matrix for significant improvement in osteoblast proliferation, endothelial formation, osteosarcoma, and bacterial inhibition, guiding better bone regeneration for post-traumatic defect repair.
MeSH term(s)	Humans ; Tissue Scaffolds ; Micelles ; Curcumin/pharmacology ; Printing, Three-Dimensional ; Bone Regeneration ; Osteosarcoma ; Bone Neoplasms ; Calcium Phosphates/pharmacology ; Anti-Bacterial Agents/pharmacology ; Osteogenesis ; Tissue Engineering
Chemical Substances	Micelles ; piperine (U71XL721QK) ; Curcumin (IT942ZTH98) ; Calcium Phosphates ; Anti-Bacterial Agents
Language	English
Publishing date	2023-09-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1500523-9
ISSN	1873-4367 ; 0927-7765
ISSN (online)	1873-4367
ISSN	0927-7765
DOI	10.1016/j.colsurfb.2023.113563
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Article ; Online: Natural medicine delivery from 3D printed bone substitutes.

Bose, Susmita / Sarkar, Naboneeta / Jo, Yongdeok

Journal of controlled release : official journal of the Controlled Release Society

2023 Volume 365, Page(s) 848–875

Abstract: Unmet medical needs in treating critical-size bone defects have led to the development of numerous innovative bone tissue engineering implants. Although additive manufacturing allows flexible patient-specific treatments by modifying topological ... ...

Abstract	Unmet medical needs in treating critical-size bone defects have led to the development of numerous innovative bone tissue engineering implants. Although additive manufacturing allows flexible patient-specific treatments by modifying topological properties with various materials, the development of ideal bone implants that aid new tissue regeneration and reduce post-implantation bone disorders has been limited. Natural biomolecules are gaining the attention of the health industry due to their excellent safety profiles, providing equivalent or superior performances when compared to more expensive growth factors and synthetic drugs. Supplementing additive manufacturing with natural biomolecules enables the design of novel multifunctional bone implants that provide controlled biochemical delivery for bone tissue engineering applications. Controlled release of naturally derived biomolecules from a three-dimensional (3D) printed implant may improve implant-host tissue integration, new bone formation, bone healing, and blood vessel growth. The present review introduces us to the current progress and limitations of 3D printed bone implants with drug delivery capabilities, followed by an in-depth discussion on cutting-edge technologies for incorporating natural medicinal compounds embedded within the 3D printed scaffolds or on implant surfaces, highlighting their applications in several pre- and post-implantation bone-related disorders.
MeSH term(s)	Humans ; Bone Substitutes/chemistry ; Tissue Scaffolds/chemistry ; Printing, Three-Dimensional ; Tissue Engineering/methods ; Bone and Bones ; Bone Regeneration
Chemical Substances	Bone Substitutes
Language	English
Publishing date	2023-12-17
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	632533-6
ISSN	1873-4995 ; 0168-3659
ISSN (online)	1873-4995
ISSN	0168-3659
DOI	10.1016/j.jconrel.2023.09.025
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Article ; Online: Hierarchical Hydration Dynamics of RNA with Nano-Water-Pool at Its Core.

Sarkar, Raju / Singh, Rishabh K / Roy, Susmita

The journal of physical chemistry. B

2023 Volume 127, Issue 31, Page(s) 6903–6919

Abstract: Many functional RNAs fold into a compact, roughly globular shape by minimizing the electrostatic repulsion between their negatively charged phosphodiester backbone. The fold of such close, compact RNA architecture is often so designed that its outer ... ...

Abstract	Many functional RNAs fold into a compact, roughly globular shape by minimizing the electrostatic repulsion between their negatively charged phosphodiester backbone. The fold of such close, compact RNA architecture is often so designed that its outer surface and complex core both are predominately populated by phosphate groups loosely sequestering bases in the intermediate layers. A number of helical junctions maintain the RNA core and its nano-water-pool. While the folding of RNA is manifested by its counterion environment composed of mixed mono- and divalent salts, the concerted role of ion and water in maintaining an RNA fold is yet to be explored. In this work, detailed atomistic simulations of SAM-I and Add Adenine riboswitch aptamers, and subgenomic flavivirus RNA (sfRNA) have been performed in a physiological mixed mono- and divalent salt environment. All three RNA systems have compact folds with a core diameter of range 1-1.7 nm. The spatiotemporal heterogeneity of RNA hydration was probed in a layer-wise manner by distinguishing the core, the intermediate, and the outer layers. The layer-wise decomposition of hydrogen bonds and collective single-particle reorientational dynamics reveal a nonmonotonic relaxation pattern with the slowest relaxation observed at the intermediate layers that involves functionally important tertiary motifs. The slowness of this intermediate layer is attributed to two types of long-resident water molecules: (i) water from ion-hydration layers and (ii) structurally trapped water (distant from ions). The relaxation kinetics of the core and the surface water essentially exposed to the phosphate groups show well-separated time scales from the intermediate layers. In the slow intermediate layers, site-specific ions and water control the functional dynamics of important RNA motifs like kink-turn, observed in different structure-probing experiments. Most interestingly, we find that as the size of the RNA core increases (SAM1 core < sfRNAcore < Add adenine core), its hydration tends to show faster relaxation. The hierarchical hydration and the layer-wise base-phosphate composition uniquely portray the globular RNA to act like a soft vesicle with a quasi-dynamic nano-water-pool at its core.
MeSH term(s)	Hydrogen Bonding ; Oligonucleotides ; Phosphates ; RNA/chemistry ; Water/chemistry ; Subgenomic RNA/chemistry
Chemical Substances	Oligonucleotides ; Phosphates ; RNA (63231-63-0) ; Water (059QF0KO0R) ; Subgenomic RNA
Language	English
Publishing date	2023-07-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c03553
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Article ; Online: Long-time-step molecular dynamics can retard simulation of protein-ligand recognition process.

Sahil, Mohammad / Sarkar, Susmita / Mondal, Jagannath

Biophysical journal

2023 Volume 122, Issue 5, Page(s) 802–816

Abstract: Molecular dynamics (MD) simulation of biologically relevant processes at realistic time scale and atomistic precision is generally limited by prohibitively large computational cost, due to its restriction of using an ultrashort integration time step (1-2 ...

Abstract	Molecular dynamics (MD) simulation of biologically relevant processes at realistic time scale and atomistic precision is generally limited by prohibitively large computational cost, due to its restriction of using an ultrashort integration time step (1-2 fs). A popular numerical recipe to reduce the associated computational burden is adopting schemes that would allow relatively longer-time-step for MD propagation. Here, we explore the perceived potential of one of the most frequently used long-time-step protocols, namely the hydrogen mass repartitioning (HMR) approach, in alleviating the computational overhead associated with simulation of the kinetic process of protein-ligand recognition events. By repartitioning the mass of heavier atoms to their linked hydrogen atoms, HMR leverages around twofold longer time step than regular simulation, holding promise of significant performance boost. However, our probe into direct simulation of the protein-ligand recognition event, one of the computationally most challenging processes, shows that long-time-step HMR MD simulations do not necessarily translate to a computationally affordable solution. Our investigations spanning cumulative 176 μs in three independent proteins (T4 lysozyme, sensor domain of MopR, and galectin-3) show that long-time-step HMR-based MD simulations can catch the ligand in its act of recognizing the native cavity. But, as a major caveat, the ligand is found to require significantly longer time to identify buried native protein cavity in an HMR MD simulation than regular simulation, thereby defeating the purpose of its usage for performance upgrade. A molecular analysis shows that the longer time required by a ligand to recognize the protein in HMR is rooted in faster diffusion of the ligand, which reduces the survival probability of decisive on-pathway metastable intermediates, thereby slowing down the eventual recognition process at the native cavity. Together, the investigation stresses careful assessment of pitfalls of long-time-step algorithms before attempting to utilize them for higher performance for biomolecular recognition simulations.
MeSH term(s)	Molecular Dynamics Simulation ; Ligands ; Proteins ; Algorithms ; Hydrogen
Chemical Substances	Ligands ; Proteins ; Hydrogen (7YNJ3PO35Z)
Language	English
Publishing date	2023-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2023.01.036
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Article ; Online: Underutilized plant sources: A hidden treasure of natural colors

Ghosh, Susmita / Sarkar, Tanmay / Chakraborty, Runu

Food Bioscience. 2023 Apr., v. 52 p.102361-

2023

Abstract: Pigments, which are naturally found in a variety of fruits and are categorized as natural dyes, are compounds that impart color to a variety of products in the food industry. Natural colorants are being used in the food industry to broaden the color ... ...

Abstract	Pigments, which are naturally found in a variety of fruits and are categorized as natural dyes, are compounds that impart color to a variety of products in the food industry. Natural colorants are being used in the food industry to broaden the color pallet. Exploration and long-term use of underutilized crops (also known as minor or neglected) are critical for dietary diversification as well as fulfilling the nutritional needs of an ever-increasing human population. In recent years, the potential for underutilized crops as an emerging source of natural colorants has gained traction in the scientific community. The predominant factors behind the exploration of unconventional plants are sustainable production, local availability, technological feasibility, cultural importance, specialty food production, and new fundamental insights. There is an urgent need to uncover and explore underutilized plants in the changing world where unfavorable climatic and human conditions endanger natural vegetation around the planet. Humans have been using plant-based pigments since ancient times. Alternative vegetal resources and the re-discovery of underutilized plants should be prioritized in the hunt for important natural colorants. This review demonstrates the potential of this underutilized natural resource to extract promising natural colorants, which can be utilized in the food industry in the future. A scientific approach as well as research regarding the investigation, utilization, the discovery of new plant species having valuable natural pigments, their actions safety, and nutritional properties, is still needed around the world.
Keywords	color ; food industry ; food production ; human population ; humans ; new species ; vegetation ; Underutilized plants ; Neglected plants ; Natural pigments ; Food colorants ; Food safety
Language	English
Dates of publication	2023-04
Publishing place	Elsevier Ltd
Document type	Article ; Online
ISSN	2212-4292
DOI	10.1016/j.fbio.2023.102361
Database	NAL-Catalogue (AGRICOLA)

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