DNA modification readers and writers and their interplay

C Rausch, FD Hastert, MC Cardoso - Journal of molecular biology, 2020 - Elsevier
Abstracts Genomic DNA is modified in a postreplicative manner and several modifications,
the enzymes responsible for their deposition as well as proteins that read these …

Design and Synthesis of Non-Peptide Mimetics Mapping the Immunodominant Myelin Basic Protein (MBP83–96) Epitope to Function as T-Cell Receptor Antagonists

MP Yannakakis, C Simal, H Tzoupis, M Rodi… - International journal of …, 2017 - mdpi.com
Encephalitogenic T cells are heavily implicated in the pathogenesis of multiple sclerosis
(MS), an autoimmune demyelinating disease of the central nervous system. Their stimulation …

Mechanisms of histone lysine-modifying enzymes: A computational perspective on the role of the protein environment

WA Cortopassi, K Kumar, F Duarte, AS Pimentel… - Journal of Molecular …, 2016 - Elsevier
Epigenetic pathways are involved in a wide range of diseases, including cancer and
neurological disorders. Specifically, histone modifying and reading processes are the most …

Influence of the number, nature and position of methyl posttranscriptional modifications on nucleobase stacking in RNA

D Kagra, AS Mahmi, NVS Kumar… - …, 2021 - Wiley Online Library
DFT calculations are employed to quantify the influence of the presence, number, nature,
and position of posttranscriptional methylation on stacking strength of RNA bases. We carry …

[HTML][HTML] In silico modeling of epigenetic-induced changes in photoreceptor cis-regulatory elements

RA Hossain, NR Dunham, RA Enke… - Molecular …, 2018 - ncbi.nlm.nih.gov
Purpose DNA methylation is a well-characterized epigenetic repressor of mRNA
transcription in many plant and vertebrate systems. However, the mechanism of this …

In silico structural modeling of multiple epigenetic marks on DNA

K Krawczyk, S Demharter, B Knapp, CM Deane… - …, 2018 - academic.oup.com
There are four known epigenetic cytosine modifications in mammals: methylation (5mC),
hydroxymethylation (5hmC), formylation (5fC) and carboxylation (5caC). The biological …

Convertible and conformationally constrained nucleic acids (C 2 NAs)

JM Escudier, C Payrastre, B Gerland… - Organic & Biomolecular …, 2019 - pubs.rsc.org
We introduce the concept of Convertible and Constrained Nucleic Acids (C2NAs). By means
of the synthesis of a stereocontrolled N-propargyl dioxo-1, 3, 2-oxaza-phosphorinane as an …

Atomic psychiatry? An essay

IP Burges Watson - Australasian Psychiatry, 2017 - journals.sagepub.com
Objective: This article aims to address the need to rethink the classification of mental illness
and to draw attention to the current use of quantum biology and its likely future use in …

Modeling of Epigenetic Modification-Induced Changes in CRX-dependent Genes cis-Regulatory Elements

RA Hossain, NR Dunham, ME Harris, TL Hutchinson… - bioRxiv, 2017 - biorxiv.org
Purpose DNA methylation is a well characterized epigenetic repressor of mRNA
transcription in many plant and vertebrate systems. However, the mechanism of this …

Novel applications for hierarchical natural move Monte Carlo simulations: from proteins to nucleic acids

S Demharter - 2016 - ora.ox.ac.uk
Biological molecules often undergo large structural changes to perform their function.
Computational methods can provide a fine-grained description at the atomistic scale …