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Article: Editorial: Advances in protein structure, function, and design.

Chowdhury, Ratul

Frontiers in bioengineering and biotechnology

2023 Volume 10, Page(s) 1108962

Language	English
Publishing date	2023-01-05
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2022.1108962
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Article ; Online: An interactive national digital surveillance system to fight against COVID-19 in Bangladesh.

Sarker, Farhana / Chowdhury, Moinul H / Ratul, Ishrak Jahan / Islam, Shariful / Mamun, Khondaker A

Frontiers in digital health

2023 Volume 5, Page(s) 1059446

Abstract: Background: COVID-19 has affected many people globally, including in Bangladesh. Due to a lack of preparedness and resources, Bangladesh has experienced a catastrophic health crisis, and the devastation caused by this deadly virus has not yet been ... ...

Abstract	Background: COVID-19 has affected many people globally, including in Bangladesh. Due to a lack of preparedness and resources, Bangladesh has experienced a catastrophic health crisis, and the devastation caused by this deadly virus has not yet been halted. Hence, precise and rapid diagnostics and infection tracing are essential for managing the condition and limiting its spread. The conventional screening procedure, such as reverse transcription polymerase chain reaction (RT-PCR), is not available in most rural areas and is time-consuming. Therefore, a data-driven intelligent surveillance system can be advantageous for rapid COVID-19 screening and risk estimation. Objectives: This study describes the design, development, implementation, and characteristics of a nationwide web-based surveillance system for educating, screening, and tracking COVID-19 at the community level in Bangladesh. Methods: The system consists of a mobile phone application and a cloud server. The data is collected by community health professionals Results: This study began in April 2020, and the results are provided in this paper till December 2022. The system has successfully completed 1,980,323 screenings. Our rule-based AI model categorized them into five separate risk groups based on the acquired patient information. According to the data, around 51% of the overall screened populations are safe, 35% are low risk, 9% are high risk, 4% are mid risk, and the remaining 1% is very high risk. The dashboard integrates all collected data from around the nation onto a single platform. Conclusion: This screening can help the symptomatic patient take immediate action, such as isolation or hospitalization, depending on the severity. This surveillance system can also be utilized for risk mapping, planning, and allocating health resources to more vulnerable areas to reduce the virus's severity.
Language	English
Publishing date	2023-05-11
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-253X
ISSN (online)	2673-253X
DOI	10.3389/fdgth.2023.1059446
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Article ; Online: Protein engineering of pores for separation, sensing, and sequencing.

Samineni, Laxmicharan / Acharya, Bibek / Behera, Harekrushna / Oh, Hyeonji / Kumar, Manish / Chowdhury, Ratul

Cell systems

2023 Volume 14, Issue 8, Page(s) 676–691

Abstract: Proteins are critical to cellular function and survival. They are complex molecules with precise structures and chemistries, which allow them to serve diverse functions for maintaining overall cell homeostasis. Since the discovery of the first enzyme in ... ...

Abstract	Proteins are critical to cellular function and survival. They are complex molecules with precise structures and chemistries, which allow them to serve diverse functions for maintaining overall cell homeostasis. Since the discovery of the first enzyme in 1833, a gamut of advanced experimental and computational tools has been developed and deployed for understanding protein structure and function. Recent studies have demonstrated the ability to redesign/alter natural proteins for applications in industrial processes of interest and to make customized, novel synthetic proteins in the laboratory through protein engineering. We comprehensively review the successes in engineering pore-forming proteins and correlate the amino acid-level biochemistry of different pore modification strategies to the intended applications limited to nucleotide/peptide sequencing, single-molecule sensing, and precise molecular separations.
MeSH term(s)	Protein Engineering ; Amino Acids ; Engineering
Chemical Substances	Amino Acids
Language	English
Publishing date	2023-08-17
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2854138-8
ISSN	2405-4720 ; 2405-4712
ISSN (online)	2405-4720
ISSN	2405-4712
DOI	10.1016/j.cels.2023.07.004
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Article ; Online: Using cocreated visually informed community mental health education in low- and middle-income countries: A case study of youth substance misuse in Assam, India.

Duara, Raginie / Chowdhury, Diptarup / Dey, Ratul / Goswami, Sangeeta / Madill, Anna

Health expectations : an international journal of public participation in health care and health policy

2022 Volume 25, Issue 4, Page(s) 1930–1944

Abstract: Introduction: Our aim is to evaluate the visually informed community mental health education materials cocreated in our research on youth substance misuse in Assam, India, and to reflect on what we might learn for similar initiatives in low- and middle- ... ...

Abstract	Introduction: Our aim is to evaluate the visually informed community mental health education materials cocreated in our research on youth substance misuse in Assam, India, and to reflect on what we might learn for similar initiatives in low- and middle-income countries. Methods: Materials consist of: (i) images participants brought to the interview; (ii) 30 posters cocreated by participants to convey key messages from their interview; (iii) six short films on the implications of addiction, and (iv) an animation of our Pathways to Recovery model. We also created a community education package that incorporated these materials. We analyse feedback from three groups of events and a social media campaign, which drew variably across our materials and engaged a range of audiences. Results: Outcomes indicate the cocreation process and focus on the visual was successful in promoting young people's voice, increasing awareness and has potential for stigma reduction. Our educational package was deemed useful in increasing awareness and has potential for prevention and treatment. Conclusions: Our case study offers insights into community mental health education in low- and middle-income countries, confirming the importance of cocreation, the usefulness of visual materials and the potential of social media campaigns while acknowledging the importance of local context in health messaging, particularly for stigmatized topics. Patient or public contribution: Service users were involved in the cocreation of the materials evaluated in this study and contributed as presenters in one of the events reported. Members of the public took part in events in which the materials were shared and provided us with the feedback analysed in this article.
MeSH term(s)	Adolescent ; Audiovisual Aids ; Community Mental Health Services ; Developing Countries/economics ; Health Education/methods ; Humans ; India ; Social Stigma ; Socioeconomic Factors ; Substance-Related Disorders/therapy
Language	English
Publishing date	2022-06-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2119434-8
ISSN	1369-7625 ; 1369-6513
ISSN (online)	1369-7625
ISSN	1369-6513
DOI	10.1111/hex.13550
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Article ; Online: Inhibiting the cGAS-STING Pathway in Ulcerative Colitis with Programmable Micelles.

Uthaman, Saji / Parvinroo, Shadi / Mathew, Ansuja Pulickal / Jia, Xinglin / Hernandez, Belen / Proctor, Alexandra / Sajeevan, Karuna Anna / Nenninger, Ariel / Long, Mary-Jane / Park, In-Kyu / Chowdhury, Ratul / Phillips, Gregory J / Wannemuehler, Michael J / Bardhan, Rizia

ACS nano

2024

Abstract: Ulcerative colitis is a chronic condition in which a dysregulated immune response contributes to the acute intestinal inflammation of the colon. Current clinical therapies often exhibit limited efficacy and undesirable side effects. Here, programmable ... ...

Abstract	Ulcerative colitis is a chronic condition in which a dysregulated immune response contributes to the acute intestinal inflammation of the colon. Current clinical therapies often exhibit limited efficacy and undesirable side effects. Here, programmable nanomicelles were designed for colitis treatment and loaded with RU.521, an inhibitor of the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway. STING-inhibiting micelles (SIMs) comprise hyaluronic acid-stearic acid conjugates and include a reactive oxygen species (ROS)-responsive thioketal linker. SIMs were designed to selectively accumulate at the site of inflammation and trigger drug release in the presence of ROS. Our
Language	English
Publishing date	2024-04-22
Publishing country	United States
Document type	Journal Article
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.3c11257
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Article ; Online: A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation.

Chowdhury, Niaz Bahar / Simons-Senftle, Margaret / Decouard, Berengere / Quillere, Isabelle / Rigault, Martine / Sajeevan, Karuna Anna / Acharya, Bibek / Chowdhury, Ratul / Hirel, Bertrand / Dellagi, Alia / Maranas, Costas / Saha, Rajib

iScience

2023 Volume 26, Issue 12, Page(s) 108400

Abstract: Climate change has adversely affected maize productivity. Thereby, a holistic understanding of metabolic crosstalk among its organs is important to address this issue. Thus, we reconstructed the first multi-organ maize metabolic model, ...

Abstract	Climate change has adversely affected maize productivity. Thereby, a holistic understanding of metabolic crosstalk among its organs is important to address this issue. Thus, we reconstructed the first multi-organ maize metabolic model,
Language	English
Publishing date	2023-11-07
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.108400
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Article ; Online: De novo design of high-affinity antibody variable regions (scFv) against the SARS-CoV-2 spike protein

Veda Sheersh Boorla / Ratul Chowdhury / Costas D. Maranas

Abstract: AbstractThe emergence of SARS-CoV-2 is responsible for the pandemic of respiratory disease known as COVID-19, which emerged in the city of Wuhan, Hubei province, China in late 2019. Both vaccines and targeted therapeutics for treatment of this disease ... ...

Abstract	AbstractThe emergence of SARS-CoV-2 is responsible for the pandemic of respiratory disease known as COVID-19, which emerged in the city of Wuhan, Hubei province, China in late 2019. Both vaccines and targeted therapeutics for treatment of this disease are currently lacking. Viral entry requires binding of the viral spike receptor binding domain (RBD) with the human angiotensin converting enzyme (ACE2). In an earlier paper1, we report on the specific residue interactions underpinning this event. Here we report on the de novo computational design of high affinity antibody variable regions through the recombination of VDJ genes targeting the most solvent-exposed ACE2-binding residues of the SARS-CoV-2 spike protein using the software tool OptMAVEn-2.02. Subsequently, we carry out computational affinity maturation of the designed prototype variable regions through point mutations for improved binding with the target epitope. Immunogenicity was restricted by preferring designs that match sequences from a 9-mer library of “human string content” (HSC)3. We generated 60 different variable region designs and report in detail on the top five that trade-off the greatest affinity for the spike epitope (quantified using the Rosetta binding energies) with low immunogenicity scores. By grafting these designed variable regions with frameworks, high-affinity monoclonal antibodies can be constructed. Having a potent antibody that can recognize the viral spike protein with high affinity would be enabling for both the design of sensitive SARS-CoV-2 detection devices and for their deployment as neutralizing antibodies.
Keywords	covid19
Publisher	biorxiv
Document type	Article ; Online
DOI	10.1101/2020.04.09.034868
Database	COVID19

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Article ; Online: Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity

Ratul Chowdhury / Veda Sheersh Boorla / Costas D. Maranas

Computational and Structural Biotechnology Journal, Vol 18, Iss , Pp 2573-

2020 Volume 2582

Abstract: SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by binding with the cell surface receptor – angiotensin converting enzyme (ACE2). We computationally contrasted the binding interactions between human ACE2 and coronavirus ... ...

Abstract	SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by binding with the cell surface receptor – angiotensin converting enzyme (ACE2). We computationally contrasted the binding interactions between human ACE2 and coronavirus spike protein receptor binding domain (RBD) of the 2002 epidemic-causing SARS-CoV-1, SARS-CoV-2, and bat coronavirus RaTG13 using the Rosetta energy function. We find that the RBD of the spike protein of SARS-CoV-2 is highly optimized to achieve very strong binding with human ACE2 (hACE2) which is consistent with its enhanced infectivity. SARS-CoV-2 forms the most stable complex with hACE2 compared to SARS-CoV-1 (23% less stable) or RaTG13 (11% less stable). Notably, we calculate that the SARS-CoV-2 RBD lowers the binding strength of angiotensin 2 receptor type I (ATR1) which is the native binding partner of ACE2 by 44.2%. Strong binding is mediated through strong electrostatic attachments with every fourth residue on the N-terminus alpha-helix (starting from Ser19 to Asn53) as the turn of the helix makes these residues solvent accessible. By contrasting the spike protein SARS-CoV-2 Rosetta binding energy with ACE2 of different livestock and pet species we find strongest binding with bat ACE2 followed by human, feline, equine, canine and finally chicken. This is consistent with the hypothesis that bats are the viral origin and reservoir species. These results offer a computational explanation for the increased infection susceptibility by SARS-CoV-2 and allude to therapeutic modalities by identifying and rank-ordering the ACE2 residues involved in binding with the virus.
Keywords	Biophysics ; SARS CoV-2 ; COVID 19 ; ATR1 ; Human ACE2 ; Biotechnology ; TP248.13-248.65 ; covid19
Subject code	500
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass.

Choi, Soyeon / Prabhakar, Pradeep K / Chowdhury, Ratul / Pendergast, Thomas H / Urbanowicz, Breeanna R / Maranas, Costas / Devos, Katrien M

Journal of experimental botany

2023 Volume 74, Issue 18, Page(s) 5532–5546

Abstract: Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of ... ...

Abstract	Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of vegetative development and therefore biomass accumulation, a key trait in bioenergy crops. No causal variants for flowering time differences between switchgrass ecotypes have, as yet, been identified. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K in a biparental F2 population and characterized the flowering-associated transcription factor gene PvHd1, an ortholog of CONSTANS in Arabidopsis and Heading date 1 in rice, as the underlying causal gene. Protein modeling predicted that a serine to glycine substitution at position 35 (p.S35G) in B-Box domain 1 greatly altered the global structure of the PvHd1 protein. The predicted variation in protein compactness was supported in vitro by a 4 °C shift in denaturation temperature. Overexpressing the PvHd1-p.35S allele in a late-flowering CONSTANS-null Arabidopsis mutant rescued earlier flowering, whereas PvHd1-p.35G had a reduced ability to promote flowering, demonstrating that the structural variation led to functional divergence. Our findings provide us with a tool to manipulate the timing of floral transition in switchgrass cultivars and, potentially, expand their cultivation range.
MeSH term(s)	Panicum/genetics ; Arabidopsis/genetics ; Quantitative Trait Loci ; Phenotype ; Amino Acids/genetics ; Flowers/genetics
Chemical Substances	Amino Acids
Language	English
Publishing date	2023-07-03
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erad255
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Article ; Online: Evaluation of strategies to narrow the product chain-length distribution of microbially synthesized free fatty acids.

Jindra, Michael A / Choe, Kisurb / Chowdhury, Ratul / Kong, Ryan / Ghaffari, Soodabeh / Sweedler, Jonathan V / Pfleger, Brian F

Metabolic engineering

2023 Volume 77, Page(s) 21–31

Abstract: The dominant strategy for tailoring the chain-length distribution of free fatty acids (FFA) synthesized by heterologous hosts is expression of a selective acyl-acyl carrier protein (ACP) thioesterase. However, few of these enzymes can generate a precise ( ...

Abstract	The dominant strategy for tailoring the chain-length distribution of free fatty acids (FFA) synthesized by heterologous hosts is expression of a selective acyl-acyl carrier protein (ACP) thioesterase. However, few of these enzymes can generate a precise (greater than 90% of a desired chain-length) product distribution when expressed in a microbial or plant host. The presence of alternative chain-lengths can complicate purification in situations where blends of fatty acids are not desired. We report the assessment of several strategies for improving the dodecanoyl-ACP thioesterase from the California bay laurel to exhibit more selective production of medium-chain free fatty acids to near exclusivity. We demonstrated that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) was an effective library screening technique for identification of thioesterase variants with favorable shifts in chain-length specificity. This strategy proved to be a more effective screening technique than several rational approaches discussed herein. With this data, we isolated four thioesterase variants which exhibited a more selective FFA distribution over wildtype when expressed in the fatty acid accumulating E. coli strain, RL08. We then combined mutations from the MALDI isolates to generate BTE-MMD19, a thioesterase variant capable of producing free fatty acids consisting of 90% of C
MeSH term(s)	Fatty Acids, Nonesterified/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Acyl Carrier Protein/genetics ; Acyl Carrier Protein/chemistry ; Acyl Carrier Protein/metabolism ; Fatty Acids/genetics ; Thiolester Hydrolases/genetics ; Thiolester Hydrolases/metabolism ; Plants
Chemical Substances	Fatty Acids, Nonesterified ; Acyl Carrier Protein ; Fatty Acids ; Thiolester Hydrolases (EC 3.1.2.-)
Language	English
Publishing date	2023-03-01
Publishing country	Belgium
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1470383-x
ISSN	1096-7184 ; 1096-7176
ISSN (online)	1096-7184
ISSN	1096-7176
DOI	10.1016/j.ymben.2023.02.012
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