QM/MM methods for biomolecular systems

HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …

Chemical and biochemical perspectives of protein lysine methylation

M Luo - Chemical reviews, 2018 - ACS Publications
Protein lysine methylation is a distinct posttranslational modification that causes minimal
changes in the size and electrostatic status of lysine residues. Lysine methylation plays …

Density-functional tight-binding: basic concepts and applications to molecules and clusters

F Spiegelman, N Tarrat, J Cuny, L Dontot… - … in physics: X, 2020 - Taylor & Francis
The scope of this article is to present an overview of the Density Functional based Tight
Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and …

Chemical mechanisms of histone lysine and arginine modifications

BC Smith, JM Denu - Biochimica et Biophysica Acta (BBA)-Gene Regulatory …, 2009 - Elsevier
Histone lysine and arginine residues are subject to a wide array of post-translational
modifications including methylation, citrullination, acetylation, ubiquitination, and …

Sphingolipids and cancer: ceramide and sphingosine-1-phosphate in the regulation of cell death and drug resistance

S Ponnusamy, M Meyers-Needham, CE Senkal… - Future …, 2010 - Taylor & Francis
Sphingolipids have emerged as bioeffector molecules, controlling various aspects of cell
growth and proliferation in cancer, which is becoming the deadliest disease in the world …

[HTML][HTML] Direct interaction between the inhibitor 2 and ceramide via sphingolipid-protein binding is involved in the regulation of protein phosphatase 2A activity and …

A Mukhopadhyay, SA Saddoughi, P Song… - The FASEB …, 2009 - ncbi.nlm.nih.gov
In this study, the inhibitor 2 of protein phosphatase 2A (I2PP2A) was identified in vitro and in
situ as a ceramide-binding protein, which exhibits stereoisomer specificity and fatty acid …

Specificity analysis-based identification of new methylation targets of the SET7/9 protein lysine methyltransferase

A Dhayalan, S Kudithipudi, P Rathert, A Jeltsch - Chemistry & biology, 2011 - cell.com
We applied peptide array methylation to determine an optimized target sequence for the
SET7/9 (KMT7) protein lysine methyltransferase. Based on this, we identified 91 new …

Biological processes and signal transduction pathways regulated by the protein methyltransferase SETD7 and their significance in cancer

IAA Batista, LA Helguero - Signal transduction and targeted therapy, 2018 - nature.com
Protein methyltransferases have been shown to methylate histone and non-histone proteins,
leading to regulation of several biological processes that control cell homeostasis. Over the …

Epigenetic modifications of Keap1 regulate its interaction with the protective factor Nrf2 in the development of diabetic retinopathy

M Mishra, Q Zhong, RA Kowluru - … ophthalmology & visual …, 2014 - iovs.arvojournals.org
Purpose.: Diabetes induces oxidative imbalance in the retina and impairs Nrf2-mediated
antioxidant response, and elevates Keap1, the cytoplasmic repressor of Nrf2. The goal of …

Cancers and the NSD family of histone lysine methyltransferases

M Morishita, E di Luccio - Biochimica et Biophysica Acta (BBA)-Reviews on …, 2011 - Elsevier
Both genetic and epigenetic alterations are responsible for the stepwise initiation and
progression of cancers. Only epigenetic aberrations can be reversible, allowing the …