Characterizing the Conformational Landscape of MDM2-binding p53 peptides using Molecular Dynamics simulations

The conformational landscapes of p53 peptide variants and phage derived peptide (12/1) variants, all known to bind to MDM2, are studied using hamiltonian replica exchange molecular dynamics simulations. Complementing earlier observations, the current study suggests that the p53 peptides largely follow the ‘conformational selection’ paradigm in their recognition of and complexation by MDM2 while the 12/1 peptides likely undergo some element of conformational selection but are mostly driven by ‘binding induced folding’.

type: 
Journal Paper
journal: 
Scientific Reports 7, Article no:15600, 2017, doi:10.1038/s41598-017-15930-4
Url: 
https://www.nature.com/articles/s41598-017-15930-4
Impact Factor: 
4.259
Date of acceptance: 
2017-11-03

Small molecules targeting the inactive form of the Mnk 1/2 kinases

Overexpression of the eukaryotic initiation factor 4E (eIF4E) is linked to a variety of cancers. Both mitogenactivated protein kinases-interacting kinases 1 and 2 (Mnk1/2) activate the oncogene eIF4E through posttranslational modification (phosphorylating it at the conserved Ser209). Inhibition of Mnk prevents eIF4E phosphorylation, making the Mnk−eIF4E axis a potential therapeutic target for oncology. Recently, the design and synthesis of a series of novel potent compounds inhibiting the Mnk1/2 kinases were carried out in-house.

type: 
Journal Paper
journal: 
ACS Omega 2017, 2, Pg 7881 - 7891, doi: 10.1021/acsomega.7b01403
Date of acceptance: 
2017-10-31

A yeast two-hybrid system for the screening and characterization of small-molecule inhibitors of protein–protein interactions identifies a novel putative Mdm2-binding site in p53

Background: Protein–protein interactions (PPIs) are fundamental to the growth and survival of cells and serve as excellent targets to develop inhibitors of biological processes such as host-pathogen interactions and cancer cell proliferation. However, isolation of PPI inhibitors is extremely challenging. While several in vitro assays to screen for PPI inhibitors are available, they are often expensive, cumbersome, and require large amounts of purified protein. In contrast, limited in vivo assays are available to screen for small-molecule inhibitors of PPI.

type: 
Journal Paper
journal: 
BMC Biology 2017 15:108, doi: 10.1186/s12915-017-0446-7
Url: 
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0446-7
Impact Factor: 
6.779
Date of acceptance: 
2017-10-19

Optimal Charge-to-Spin Conversion in Graphene on Transition-Metal Dichalcogenides

When graphene is placed on a monolayer of semiconducting transition metal dichalcogenide (TMD) its band structure develops rich spin textures due to proximity spin-orbital effects with interfacial breaking of inversion symmetry. In this work, we show that the characteristic spin winding of low-energy states in graphene on a TMD monolayer enables current-driven spin polarization, a phenomenon known as the inverse spin galvanic effect (ISGE).

type: 
Journal Paper
journal: 
Physical Review Letters, Vol. 114, Issue 119, 10 Nov 2017, doi: 10.1103/PhysRevLett.119.196801
Url: 
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.196801
Impact Factor: 
8.462

High-throughput Prediction of Nephrotoxicity in Humans

The Lush Science Prize 2016 was awarded to Daniele Zink and Lit-Hsin Loo for the interdisciplinary
and collaborative work between their research groups in developing alternative methods for the
prediction of nephrotoxicity in humans. The collaboration has led to the establishment of a series of pioneering alternative methods for nephrotoxicity prediction, which includes: predictive gene expression
markers based on pro-inflammatory responses; predictive in vitro cellular models based on pluripotent

type: 
Journal Paper
journal: 
ATLA 45, Pg 241-252, 5 Nov 2017
Url: 
http://www.atla.org.uk/high-throughput-prediction-of-nephrotoxicity-in-humans/
Impact Factor: 
1.021

APD volumetric app: android app for the quantification of reagents

Quantifying reagents is a necessity in laboratory experiment planning but to do so with reasonable accuracy is a challenge when using unmarked containers. While there are volumetric measuring cylinders, the demand of sterility and purity in many experiments prevent their use in a feasible fashion. As a result, experienced estimation is usually relied upon, but this is fairly subjective, and may lead to large margins of error.

type: 
Journal Paper
journal: 
Scientific Phone Apps and Mobile Devices (2017) 3:7, doi: 10.1186/s41070-017-0019-8
Url: 
https://scientificphoneapps.springeropen.com/articles/10.1186/s41070-017-0019-8
Date of acceptance: 
2017-10-11

Inter-Species Host Gene Expression Differences in Response to Human and Avian Influenza A Virus Strains

Low pathogenic avian influenza (LPAI) viruses are a source of sporadic human infections and could also contribute to future pandemic outbreaks but little is known about inter-species differences in the host responses to these viruses. Here, we studied host gene expression signatures of cell lines from three species (human, chicken, and canine) in response to six different viruses (H1N1/WSN, H5N2/F59, H5N2/F118, H5N2/F189, H5N3 and H9N2).

type: 
Journal Paper
journal: 
International Journal of Molecular Sciences, Vol. 18, Issue 11, doi: 10.3390/ijms18112295
pubmed: 
29104227
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/29104227
Impact Factor: 
3.226
Date of acceptance: 
2017-10-25

Multiview and Multimodal Pervasive Indoor Localization

Pervasive indoor localization (PIL) aims to locate an indoor mobile-phone user without any infrastructure assistance. Conventional PIL approaches employ a single probe (i.e., target) measurement to localize by identifying its best match out of a fingerprint gallery. However, a single measurement usually captures limited and inadequate location features. More importantly, the reliance on a single measurement bears the inherent risk of being inaccurate and unreliable, due to the fact that the measurement could be noisy and even corrupted.

type: 
Conference Paper/Poster
journal: 
Multi Media 17, Proceedings of the 2017 ACM on Multimedia Conference, Pg 109-117. Mountain view, California, USA, Oct 23-27 2017, doi: 10.1145/3123266.3123436
Url: 
https://dl.acm.org/citation.cfm?id=3123266.3123436
Date of acceptance: 
2017-12-29

Multiview and Multimodal Pervasive Indoor Localization

Pervasive indoor localization (PIL) aims to locate an indoor mobile-phone user without any infrastructure assistance. Conventional PIL approaches employ a single probe (i.e., target) measurement to localize by identifying its best match out of a fingerprint gallery. However, a single measurement usually captures limited and inadequate location features. More importantly, the reliance on a single measurement bears the inherent risk of being inaccurate and unreliable, due to the fact that the measurement could be noisy and even corrupted.

type: 
Conference Paper/Poster
journal: 
"Multi Media 17, Proceedings of the 2017 ACM on Multimedia Conference, Pg 109-117. Mountain view, California, USA, Oct 23-27 2017, doi: 10.1145/3123266.3123436 "
Url: 
https://dl.acm.org/citation.cfm?id=3123266.3123436

Evaluation of tools for long read RNA-seq splice-aware alignment

MOTIVATION:

type: 
Journal Paper
journal: 
Bioinformatics, 2017, Pg 1-7, doi: 10.1093/bioinformatics/btx668
pubmed: 
29069314
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/29069314
Impact Factor: 
7.037
Date of acceptance: 
2017-10-18
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