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Article ; Online: Why Are Nucleosome Breathing Dynamics Asymmetric?

Mondal, Anupam / Kolomeisky, Anatoly B

The journal of physical chemistry letters

2024 Volume 15, Issue 2, Page(s) 422–431

Abstract: In eukaryotic cells, DNA is bound to nucleosomes, but DNA segments occasionally unbind in the process known as nucleosome breathing. Although DNA can unwrap simultaneously from both ends of the nucleosome (symmetric breathing), experiments indicate that ... ...

Abstract	In eukaryotic cells, DNA is bound to nucleosomes, but DNA segments occasionally unbind in the process known as nucleosome breathing. Although DNA can unwrap simultaneously from both ends of the nucleosome (symmetric breathing), experiments indicate that DNA prefers to dissociate from only one end (asymmetric breathing). However, the molecular origin of the asymmetry is not understood. We developed a new theoretical approach that gives microscopic explanations of asymmetric breathing. It is based on a stochastic description that leads to a comprehensive evaluation of dynamics by using effective free-energy landscapes. It is shown that asymmetric breathing follows the kinetically preferred pathways. In addition, it is also found that asymmetric breathing leads to a faster target search by transcription factors. Theoretical predictions, supported by computer simulations, agree with experiments. It is proposed that nature utilizes the symmetry of nucleosome breathing to achieve a better dynamic accessibility of chromatin for more efficient genetic regulation.
MeSH term(s)	Nucleosomes ; Chromatin ; DNA/metabolism ; Transcription Factors ; Computer Simulation
Chemical Substances	Nucleosomes ; Chromatin ; DNA (9007-49-2) ; Transcription Factors
Language	English
Publishing date	2024-01-05
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.3c03339
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Article ; Online: Role of Nucleosome Sliding in the Protein Target Search for Covered DNA Sites.

Mondal, Anupam / Kolomeisky, Anatoly B

The journal of physical chemistry letters

2023 Volume 14, Issue 31, Page(s) 7073–7082

Abstract: Associations of transcription factors (TFs) with specific sites on DNA initiate major cellular processes. But DNA in eukaryotic cells is covered by nucleosomes which prevent TFs from binding. However, nucleosome structures on DNA are not static and ... ...

Abstract	Associations of transcription factors (TFs) with specific sites on DNA initiate major cellular processes. But DNA in eukaryotic cells is covered by nucleosomes which prevent TFs from binding. However, nucleosome structures on DNA are not static and exhibit breathing and sliding. We develop a theoretical framework to investigate the effect of nucleosome sliding on a protein target search. By analysis of a discrete-state stochastic model of nucleosome sliding, search dynamics are explicitly evaluated. It is found that for long sliding lengths the target search dynamics are faster for normal TFs that cannot enter the nucleosomal DNA. But for more realistic short sliding lengths, the so-called pioneer TFs, which can invade nucleosomal DNA, locate specific sites faster. It is also suggested that nucleosome breathing, which is a faster process, has a stronger effect on protein search dynamics than that of nucleosome sliding. Theoretical arguments to explain these observations are presented.
MeSH term(s)	Nucleosomes ; Transcription Factors ; DNA/chemistry ; Binding Sites
Chemical Substances	Nucleosomes ; Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2023-08-01
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.3c01704
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Article: Network Biology and Medicine to Rescue: Applications for Retinal Disease Mechanisms and Therapy.

Mondal, Anupam K / Swaroop, Anand

Advances in experimental medicine and biology

2023 Volume 1415, Page(s) 165–171

Abstract: Inherited retinal degenerations (IRDs) are clinically and genetically heterogenous blinding diseases that manifest through dysfunction of target cells, photoreceptors, and retinal pigment epithelium (RPE) in the retina. Despite knowledge of numerous ... ...

Abstract	Inherited retinal degenerations (IRDs) are clinically and genetically heterogenous blinding diseases that manifest through dysfunction of target cells, photoreceptors, and retinal pigment epithelium (RPE) in the retina. Despite knowledge of numerous underlying genetic defects, current therapeutic approaches, including gene centric applications, have had limited success, thereby asserting the need of new directions for basic and translational research. Human diseases have commonalities that can be represented in a network form, called diseasome, which captures relationships among disease genes, proteins, metabolites, and patient meta-data. Clinical and genetic information of IRDs suggest shared relationships among pathobiological factors, making these a model case for network medicine. Characterization of the diseasome would considerably improve our understanding of retinal pathologies and permit better design of targeted therapies for disrupted regions within the integrated disease network. Network medicine in synergy with the ongoing artificial intelligence revolution can boost therapeutic developments, especially gene agnostic treatment opportunities.
MeSH term(s)	Humans ; Artificial Intelligence ; Retina/pathology ; Retinal Degeneration/genetics ; Retinal Degeneration/therapy ; Retinal Degeneration/pathology ; Retinal Pigment Epithelium/pathology ; Biology
Language	English
Publishing date	2023-07-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	410187-X
ISSN	0065-2598
ISSN	0065-2598
DOI	10.1007/978-3-031-27681-1_25
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Article ; Online: Nucleosome Breathing Facilitates the Search for Hidden DNA Sites by Pioneer Transcription Factors.

Mondal, Anupam / Felipe, Cayke / Kolomeisky, Anatoly B

The journal of physical chemistry letters

2023 Volume 14, Issue 17, Page(s) 4096–4103

Abstract: Transfer of genetic information starts with transcription factors (TFs) binding to specific sites on DNA. But in living cells, DNA is mostly covered by nucleosomes. There are proteins, known as pioneer TFs, that can efficiently reach the DNA sites hidden ...

Abstract	Transfer of genetic information starts with transcription factors (TFs) binding to specific sites on DNA. But in living cells, DNA is mostly covered by nucleosomes. There are proteins, known as pioneer TFs, that can efficiently reach the DNA sites hidden by nucleosomes, although the underlying mechanisms are not understood. Using the recently proposed idea of interaction-compensation mechanism, we develop a stochastic model for the target search on DNA with nucleosome breathing. It is found that nucleosome breathing can significantly accelerate the search by pioneer TFs in comparison to situations without breathing. We argue that this is the result of the interaction-compensation mechanism that allows proteins to enter the inner nucleosome region through the outer DNA segment. It is suggested that nature optimized pioneer TFs to take advantage of nucleosome breathing. The presented theoretical picture provides a possible microscopic explanation for the successful invasion of nucleosome-buried genes.
MeSH term(s)	Nucleosomes ; Transcription Factors ; Protein Binding ; DNA/metabolism ; Binding Sites
Chemical Substances	Nucleosomes ; Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2023-04-26
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.3c00529
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Article: Tea and its phytochemicals: Hidden health benefits & modulation of signaling cascade by phytochemicals

Bag, Sagar / Mondal, Anupam / Majumder, Anusha / Banik, Avishek

Food chemistry. 2022 Mar. 01, v. 371

2022

Abstract: Tea, one of the most widely consumed beverages, is prepared from the leaves of the Camellia sinensis. The promising health recompenses of tea have been linked to its different phenolic components, which have diverse biological characteristics. Tea also ... ...

Abstract	Tea, one of the most widely consumed beverages, is prepared from the leaves of the Camellia sinensis. The promising health recompenses of tea have been linked to its different phenolic components, which have diverse biological characteristics. Tea also contains several flavonoids, alkaloids, phenolic, theanine, etc., which are associated with anti-oxidant characteristics and a variety of health benefits. It can also lower the pervasiveness of neurological disorders as well as prevent different types of cancer, metabolic syndromes, cardiovascular diseases, urinary stone, obesity, type 2 diabetes. Keeping in mind that tea helps to improve health and prevents many diseases, its consumption has been regarded as a “health-promoting habit” and current medical investigators have established the scientific basis for this concept over time. The current review provides new updated information and perspectives on the tea phytochemicals and their overall health benefits based on molecular processes, experimental studies, and clinical trials.
Keywords	Camellia sinensis ; antioxidants ; flavonoids ; food chemistry ; noninsulin-dependent diabetes mellitus ; obesity ; tea ; theanine ; urinary calculi
Language	English
Dates of publication	2022-0301
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2021.131098
Database	NAL-Catalogue (AGRICOLA)

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Article: Exploring tea (Camellia sinensis) microbiome: Insights into the functional characteristics and their impact on tea growth promotion

Bag, Sagar / Mondal, Anupam / Banik, Avishek

Microbiological research. 2022 Jan., v. 254

2022

Abstract: Tea (Camellia sinensis) is perhaps the most popular and economic beverage in the globe due to its distinctive fragrance and flavour generated by the leaves of commercially farmed tea plants. The tea microbiome has now become a prominent topic of ... ...

Abstract	Tea (Camellia sinensis) is perhaps the most popular and economic beverage in the globe due to its distinctive fragrance and flavour generated by the leaves of commercially farmed tea plants. The tea microbiome has now become a prominent topic of attention for microbiologists in recent years as it can help the plant for soil nutrient acquisition as well as stress management. Tea roots are well known to be colonized by Arbuscular Mycorrhizal Fungi (AMF) and many other beneficial microorganisms that boost the growth of the tea which increases leaf amino acids, protein, caffeine, and polyphenols content. One of the primary goals of rhizosphere microbial biology is to aid in the establishment of agricultural systems that provide high quantities of the food supply while minimizing environmental effects and anthropogenic activities. The present review is aimed to highlight the importance of microbes (along with their phylogeny) derived from cultivated and natural tea rhizospheres to understand the role of AMF and rhizospheric bacterial population to improve plant growth, enhancement of tea quality, and protecting tea plants from pathogens. This review also summarizes recent advances in our understanding of the diversity and profile of tea-associated bacteria. The utilization of the tea microbiome as a “natural resource” could provide holistic development in tea cultivation to ensure sustainability, highlighting knowledge gaps and future microbiome research.
Keywords	Camellia sinensis ; beverages ; caffeine ; flavor ; food availability ; growth promotion ; leaves ; microbiome ; odors ; phylogeny ; plant growth ; polyphenols ; research ; rhizosphere ; soil nutrients ; stress management ; tea ; vesicular arbuscular mycorrhizae
Language	English
Dates of publication	2022-01
Publishing place	Elsevier GmbH
Document type	Article
ZDB-ID	1189614-0
ISSN	1618-0623 ; 0944-5013
ISSN (online)	1618-0623
ISSN	0944-5013
DOI	10.1016/j.micres.2021.126890
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Article ; Online: Characterization of a biofilm-forming, amylase-producing, and heavy-metal-bioremediating strain Micrococcus sp. BirBP01 isolated from oligotrophic subsurface lateritic soil.

Pandit, Baishali / Moin, Abdul / Mondal, Anupam / Banik, Avishek / Alam, Masrure

Archives of microbiology

2023 Volume 205, Issue 11, Page(s) 351

Abstract: Lateritic soil is the reddish to brown-colored soil composed mainly of iron or aluminium oxides, hydroxides, or oxyhydroxides. Information on bacteria that inhabit this soil type, their ecological role, and metabolic potential are scarce. We have ... ...

Abstract	Lateritic soil is the reddish to brown-colored soil composed mainly of iron or aluminium oxides, hydroxides, or oxyhydroxides. Information on bacteria that inhabit this soil type, their ecological role, and metabolic potential are scarce. We have isolated and partially characterized a bacterial strain BirBP01 from a lead, calcium, and magnesium-rich, oligotrophic subsurface lateritic soil-sample collected from 12-feet deep horizon of a laterite mining pit in Birbhum district, India. The isolate is a biofilm-forming, Gram-positive bacterium having a sarcinae arrangement, mesophilic, slightly alkaliphilic, able to produce amylase, and resistant against multiple heavy-metals. BirBP01 has the ability to bioremediate 51% of Pb, 30% of Zn, and 22% of Cu through biosorption, possibly into the biofilm matrix. The bioremediating ability of the bacterium alleviated the inhibitory effect of heavy-metals on the germination of chickpea (Cicer arietinum L.) seeds. 16S rRNA gene-based phylogenetic analysis revealed that BirBP01 is a member of the genus Micrococcus. It showed more than 99% identity of the 16S rRNA gene sequence, and clustered within the same branch of the phylogenetic tree, with strains of M. yunnanensis, M. endophyticus, and M. luteus. The ability to produce amylase, and bioremediate heavy-metals signify that Micrococcus sp. BirBP01 could be potentially a good candidate for industrial applications, and to clean up heavy-metal contaminated sites.
MeSH term(s)	Micrococcus/genetics ; Micrococcus/metabolism ; Soil ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metals, Heavy/metabolism ; Bacteria/genetics ; Biofilms ; Soil Pollutants/metabolism ; Biodegradation, Environmental
Chemical Substances	Soil ; RNA, Ribosomal, 16S ; Metals, Heavy ; Soil Pollutants
Language	English
Publishing date	2023-10-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	124824-8
ISSN	1432-072X ; 0302-8933
ISSN (online)	1432-072X
ISSN	0302-8933
DOI	10.1007/s00203-023-03690-x
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Article ; Online: Antibacterial, antibiofilm and larvicidal activity of silver nanoparticles synthesized from spider silk protein.

Mondal, Anupam / Maity, Suprity / Mondal, Arghadip / Mondal, Naba Kumar

International journal of biological macromolecules

2023 Volume 258, Issue Pt 1, Page(s) 128775

Abstract: Green synthesis of silver nanoparticles has gained attention due to its simple process of synthesis and varied applications. Scientists have tried its synthesis from a wide range of materials, but there is lack of reports that can use the metabolites of ... ...

Abstract	Green synthesis of silver nanoparticles has gained attention due to its simple process of synthesis and varied applications. Scientists have tried its synthesis from a wide range of materials, but there is lack of reports that can use the metabolites of insects. Here in this study, we have used the spider silk protein which is considered as complete waste collected from household and field sources and processed to synthesize silver nanoparticles which were subsequently analyzed using different analytical tools like SEM, TEM, FTIR, and XRD. The spider silk protein-mediated synthesized nanoparticle (SP-AgNPs) showed a sharp peak at 420 nm when analyzed spectrophotometrically giving an indication of successful synthesis of AgNP. The synthesized nanoparticle ranges from 10 to 40 nm and were of varied shapes. The synthesized SP-AgNPs showed remarkable antibacterial activity. The MIC values against B. subtilis and E. coli were recorded 45 and 40 μg/mL respectively. Further to know the mechanisms of antibacterial activity protein leakage and conductivity measurement were conducted. The synthesized nanoparticle also showed excellent antibiofilm activity with inhibition percentages of 74 % and 68 % for E. coli and B. subtilis respectively at MIC concentration of the treatment. Finally, the synthesized nanoparticles was applied as mosquito larvicidal agent against Culex sp. and the difference between LC
MeSH term(s)	Animals ; Anti-Bacterial Agents/pharmacology ; Biofilms ; Escherichia coli ; Insecticides/pharmacology ; Larva ; Metal Nanoparticles ; Silk/chemistry ; Silver/pharmacology ; Culex
Chemical Substances	Anti-Bacterial Agents ; Insecticides ; Silk ; Silver (3M4G523W1G)
Language	English
Publishing date	2023-12-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.128775
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Article ; Online: Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.

Mondal, Anupam / Mishra, Sujeet Kumar / Bhattacherjee, Arnab

Biophysical journal

2022 Volume 121, Issue 23, Page(s) 4526–4542

Abstract: Critical lineage commitment events are staged by multiple transcription factors (TFs) binding to their cognate motifs, often positioned at nucleosome-enriched regions of chromatin. The underlying mechanism remains elusive due to difficulty in ... ...

Abstract	Critical lineage commitment events are staged by multiple transcription factors (TFs) binding to their cognate motifs, often positioned at nucleosome-enriched regions of chromatin. The underlying mechanism remains elusive due to difficulty in disentangling the heterogeneity in chromatin states. Using a novel coarse-grained model and molecular dynamics simulations, here we probe the association of Sox2 and Oct4 proteins that show clustered binding at the entry-exit region of a nucleosome. The model captures the conformational heterogeneity of nucleosome breathing dynamics that features repeated wrap-unwrap transitions of a DNA segment from one end of the nucleosome. During the dynamics, DNA forms bulges that diffuse stochastically and may regulate the target search dynamics of a protein by nonspecifically interacting with it. The overall search kinetics of the TF pair follows a "dissociation-compensated-association" mechanism, where Oct4 binding is facilitated by the association of Sox2. The cooperativity stems from a change in entropy caused by an alteration in the nucleosome dynamics upon TF binding. The binding pattern is consistent with a live-cell single-particle tracking experiment, suggesting the mechanism observed for clustered binding of a TF pair, which is a hallmark of cis-regulatory elements, has broader implications in understanding gene regulation in a complex chromatin environment.
MeSH term(s)	Nucleosomes ; DNA
Chemical Substances	Nucleosomes ; DNA (9007-49-2)
Language	English
Publishing date	2022-11-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2022.10.039
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Article ; Online: Mechanism of Dynamic Binding of Replication Protein A to ssDNA.

Mondal, Anupam / Bhattacherjee, Arnab

Journal of chemical information and modeling

2020 Volume 60, Issue 10, Page(s) 5057–5069

Abstract: Replication protein A (RPA) serves as a hub protein inside eukaryotic cells, where it coordinates crucial DNA metabolic processes and activates the DNA-damage response system. A characteristic feature of its action is to associate with single-stranded ... ...

Abstract	Replication protein A (RPA) serves as a hub protein inside eukaryotic cells, where it coordinates crucial DNA metabolic processes and activates the DNA-damage response system. A characteristic feature of its action is to associate with single-stranded DNA (ssDNA) intermediates before handing them over to downstream proteins. The length of ssDNA intermediates differs for different pathways. This means that RPA must have mechanisms for selective processing of ssDNA intermediates based on their length, the knowledge of which is fundamental to elucidate when and how DNA repair and replication processes are symphonized. By employing extensive molecular dynamics simulations, we investigated the mechanism of binding of RPA to ssDNA of different lengths. We show that the binding involves dynamic equilibrium with a stable intermediate, the population of which increases with the length of ssDNA. The vital underlying factors are decoded through collective variable principal component analysis. It suggests a differently orchestrated set of interactions that define the action of RPA based on the length of ssDNA intermediates. We further estimated the association kinetics that matches excellently well with previous experimental studies and probed the diffusion mechanism of RPA to ssDNA. RPA diffuses on short ssDNA through progressive "bulge" formation. With long ssDNA, we observed a conformational change in ssDNA coupled with its binding to RPA in a cooperative fashion. This unanticipated binding mechanism successfully explains how the "short-lived", long ssDNA intermediates are processed quickly in vivo. This study thus reveals the molecular basis of several recent experimental observations related to RPA binding to ssDNA and provides novel insights into the RPA functioning in DNA repair and replication.
MeSH term(s)	DNA Repair ; DNA Replication ; DNA, Single-Stranded ; Protein Binding ; Replication Protein A/genetics ; Replication Protein A/metabolism
Chemical Substances	DNA, Single-Stranded ; Replication Protein A
Language	English
Publishing date	2020-10-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.0c00564
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