Methods and Applications in Proteins and RNAs

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Proteins and Proteomics".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 3037

Special Issue Editors


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Guest Editor
Department of Physics, Institute of Biophysics, Central China Normal University, Wuhan 430079, China
Interests: structure prediction; regulation mechanisms; drug design
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
Interests: integrated computational biology; NMR; Protein/RNA structure modeling; MD simulation

Special Issue Information

Dear Colleagues,

The rapid advancement in techniques brings to the forefront the race to understand the functions and mechanisms of disease at a molecular level. Cutting-edge methods have been developed to solve challenging problems in biology. Atomic simulations, coarse-grained models, and other computational scenarios with experimental information have significantly accelerated scientific discoveries in biological as well as medical research and successfully implemented them to study health-related problems. This topic aims to bring researchers from multidisciplinary backgrounds together to share their expertise in diverse aspects of methods and applications of proteins and RNAs. The themes will be centered around computational methods in biological and medical research. This topic ranges from structure perdition/simulation, new computational methodologies, experiments, and platforms to facilitate data sharing to the applications of multi-omics approaches.

Dr. Yunjie Zhao
Dr. Zhou Gong
Guest Editors

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Keywords

  • molecular dynamic simulations
  • deep learning algorithms
  • structural modeling/simulation with experimental data
  • software or database development for biology research
  • protein/RNA tertiary structure prediction or design
  • protein–protein/DNA/RNA complex structure prediction
  • drug design
  • applications in health, food, and agriculture

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Published Papers (2 papers)

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Editorial

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2 pages, 186 KiB  
Editorial
Methods and Applications in Proteins and RNAs
by Haoquan Liu, Zhou Gong and Yunjie Zhao
Life 2023, 13(3), 672; https://doi.org/10.3390/life13030672 - 1 Mar 2023
Cited by 2 | Viewed by 1056
Abstract
Proteins and RNAs are primary biomolecules that are involved in most biological processes [...] Full article
(This article belongs to the Special Issue Methods and Applications in Proteins and RNAs)

Research

Jump to: Editorial

11 pages, 3982 KiB  
Article
Phosphorylation of Tyrosine 841 Plays a Significant Role in JAK3 Activation
by Shengjie Sun, Georgialina Rodriguez, Yixin Xie, Wenhan Guo, Alan E. Lopez Hernandez, Jason E. Sanchez, Robert Arthur Kirken and Lin Li
Life 2023, 13(4), 981; https://doi.org/10.3390/life13040981 - 10 Apr 2023
Cited by 3 | Viewed by 1358
Abstract
Janus Kinase 3 (JAK3) plays a key role in the development, proliferation, and differentiation of various immune cells. It regulates gene expression by phosphorylation of Signal Transducers and Activators of Transcriptions (STATs) via the JAK/STAT pathway. Recently, we found a new JAK3 phosphorylation [...] Read more.
Janus Kinase 3 (JAK3) plays a key role in the development, proliferation, and differentiation of various immune cells. It regulates gene expression by phosphorylation of Signal Transducers and Activators of Transcriptions (STATs) via the JAK/STAT pathway. Recently, we found a new JAK3 phosphorylation site, tyrosine 841 (Y841). The results showed that pY841 helps the kinase domain flip around the pseudo kinase domain, which may cause JAK3 conformational changes. It also reduces the size of the cleft between the N-lobe and the C-lobe of the JAK3 kinase domain. However, pY841 was found to enlarge the cleft when ATP/ADP was bound to the kinase. The increase in the cleft size suggested that pY841 enhanced the elasticity of the kinase domain. For unphosphorylated JAK3 (JAK3-Y841), the binding forces between the kinase domain and ATP or ADP were similar. After phosphorylation of Y841, JAK3-pY841 exhibited more salt bridges and hydrogen bonds between ATP and the kinase than between ADP and the kinase. Consequently, the electrostatic binding force between ATP and the kinase was higher than that between ADP and the kinase. The result was that compared to ADP, ATP was more attractive to JAK3 when Y841 was phosphorylated. Therefore, JAK3-pY841 tended to bind ATP rather than ADP. This work provides new insights into the role of phosphorylation in kinase activation and ATP hydrolysis and sheds light on the importance of understanding the molecular mechanisms that regulate the kinase function. Full article
(This article belongs to the Special Issue Methods and Applications in Proteins and RNAs)
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