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Articles by Prem Chapagain
SPNS2 exports sphingosine-1-phosphate and imports glucose
Abstract Spinster homolog 2 (SPNS2) exports the bioactive sphingolipid metabolite sphingosine-1-phosphate (S1P) out of cells to regulate processes important for health and diseases. However, the molecular mechanism underlying SPNS2 transport functions and its precise physiological roles are not fully understood.
Weather information sources, sharing platforms, and trustworthiness for climate change adaptation in Bangladesh, India, and Nepal
ABSTRACT Reliable weather information plays a greater role in agricultural decision-making and enhances adaptive capacity to climate change among farming communities. Timely weather information, pertinent understanding, and utilization support farming activities and build the resilience of smallholder farmers. This study presents a comparative analysis of sources, trustworthiness, sharing mechanisms, and use of weather information in farming practices in Bangladesh, India, and Nepal.
Mapping the Interactions Among Class IIa Histone Deacetylases and Myocyte Enhancer Factor 2s
1. Introduction Click to copy section linkSection link copied! Myocyte enhancer factor 2 (MEF2) transcription factors are highly expressed in cerebellar granule neurons (CGNs), (1) regulate several developmental programs that include control of neural crest development, neuronal differentiation, and neuronal survival. (2−6) MEF2A, MEF2B, MEF2C, and MEF2D are four different types of human MEF2s. (6) MEF2s form dimer (7) mediated by the MADS (MCM1, agamous, deficiens, SRF) and MEF2 domains.
Characterization of molecular interactions between HDAC7 and MEF2A
Abstract Interactions of transcriptional corepressors such as histone deacetylase 7 (HDAC7), a class IIa HDAC, with myocyte enhancer factor-2 (MEF2) regulate MEF2 activity. Despite previous investigations exploring interactions between HDAC7 and MEF2, a detailed characterization of the HDAC7-MEF2 functional complex is still lacking. Herein, we first modeled the structure of the HDAC7-MEF2A complex and investigated the inter-protein interactions using all-atom molecular dynamics (MD) simulations.
Minor electrostatic changes robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles
Abstract Ebola virus (EBOV) is a filamentous negative-sense RNA virus which causes severe hemorrhagic fever. There are limited vaccines or therapeutics for prevention and treatment of EBOV, so it is important to get a detailed understanding of the virus lifecycle to illuminate new drug targets. EBOV encodes for the matrix protein, VP40, which regulates assembly and budding of new virions from the inner leaflet of the host cell plasma membrane (PM).
Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations
Special Issue Published as part of Journal of Chemical Information and Modeling virtual special issue “Editing DNA and RNA through Computations”. Topoisomerases are enzymes found in all domains of life and are responsible for resolving topological barriers in DNA that arise during vital cellular activities such as transcription, DNA replication, and recombination.
Minor changes in electrostatics robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles
Abstract Ebola virus (EBOV) is a filamentous negative-sense RNA virus which causes severe hemorrhagic fever. There are limited vaccines or therapeutics for prevention and treatment of EBOV, so it is important to get a detailed understanding of the virus lifecycle to illuminate new drug targets. EBOV encodes for the matrix protein, VP40, which regulates assembly and budding of new virions from the inner leaflet of the host cell plasma membrane (PM).
Evaluating protein binding interfaces with transformer networks - Nature Machine Intelligence
Abstract Computational protein-binding studies are widely used to investigate fundamental biological processes and facilitate the development of modern drugs, vaccines and therapeutics. Scoring functions aim to assess and rank the binding strength of the predicted protein complex. However, accurate scoring of protein binding interfaces remains a challenge.
IJMS | Free Full-Text | Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding
Open AccessArticle by 1, 1,2 and 1,2,* 1 Department of Physics, Florida International University, Miami, FL 33199, USA 2 Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA * Author to whom correspondence should be addressed. Int. J. Mol. Sci.
PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks
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PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
Effects of sidechain isomerism on polymer-based non-covalent protein delivery
Effects of sidechain isomerism on polymer-based non-covalent protein delivery† Alfonso Barrios,a Mario Milan,a Elianny Perozo,a Md Lokman Hossen, b Prem Chapagain bc and Joong Ho Moon *ac Abstract We present the importance of functional group isomerism on intracellular protein delivery using polymers containing different isomeric side chains.
The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection:
Highlights • SARS-CoV-2 spike protein binds to α5β1 integrin protein and human ACE2/α5β1, facilitating entry into host cells. • ATN-161, an integrin binding peptide, inhibits the interaction between the SARS-CoV-2 spike protein and its host binding partners, with 3 sites of binding identified via molecular modeling. • ATN-161 inhibits infection in vitro and demonstrates increases in cell viability when administered prophylactically.
Single‐stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation - Porter - - Rapid Communications in Mass Spectrometry - Wiley Online Library
The full text of this article hosted at iucr.org is unavailable due to technical difficulties.
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