TY  - JOUR
A1  - Salihoglu, Rana
A1  - Srivastava, Mugdha
A1  - Liang, Chunguang
A1  - Schilling, Klaus
A1  - Szalay, Aladar
A1  - Bencurova, Elena
A1  - Dandekar, Thomas
T1  - PRO-Simat: Protein network simulation and design tool
JF  - Computational and Structural Biotechnology Journal
N2  - PRO-Simat is a simulation tool for analysing protein interaction networks, their dynamic change and pathway engineering. It provides GO enrichment, KEGG pathway analyses, and network visualisation from an integrated database of more than 8 million protein-protein interactions across 32 model organisms and the human proteome. We integrated dynamical network simulation using the Jimena framework, which quickly and efficiently simulates Boolean genetic regulatory networks. It enables simulation outputs with in-depth analysis of the type, strength, duration and pathway of the protein interactions on the website. Furthermore, the user can efficiently edit and analyse the effect of network modifications and engineering experiments. In case studies, applications of PRO-Simat are demonstrated: (i) understanding mutually exclusive differentiation pathways in Bacillus subtilis, (ii) making Vaccinia virus oncolytic by switching on its viral replication mainly in cancer cells and triggering cancer cell apoptosis and (iii) optogenetic control of nucleotide processing protein networks to operate DNA storage. Multilevel communication between components is critical for efficient network switching, as demonstrated by a general census on prokaryotic and eukaryotic networks and comparing design with synthetic networks using PRO-Simat. The tool is available at https://prosimat.heinzelab.de/ as a web-based query server.
KW  - network simulation
KW  - protein analysis
KW  - signalling pathways
KW  - dynamic protein-protein interactions
KW  - optogenetics
KW  - oncolytic virus
KW  - DNA storage
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-350034
SN  - 2001-0370
VL  - 21
ER  - 
TY  - JOUR
A1  - Bencurova, Elena
A1  - Shityakov, Sergey
A1  - Schaack, Dominik
A1  - Kaltdorf, Martin
A1  - Sarukhanyan, Edita
A1  - Hilgarth, Alexander
A1  - Rath, Christin
A1  - Montenegro, Sergio
A1  - Roth, Günter
A1  - Lopez, Daniel
A1  - Dandekar, Thomas
T1  - Nanocellulose composites as smart devices with chassis, light-directed DNA Storage, engineered electronic properties, and chip integration
JF  - Frontiers in Bioengineering and Biotechnology
N2  - The rapid development of green and sustainable materials opens up new possibilities in the field of applied research. Such materials include nanocellulose composites that can integrate many components into composites and provide a good chassis for smart devices. In our study, we evaluate four approaches for turning a nanocellulose composite into an information storage or processing device: 1) nanocellulose can be a suitable carrier material and protect information stored in DNA. 2) Nucleotide-processing enzymes (polymerase and exonuclease) can be controlled by light after fusing them with light-gating domains; nucleotide substrate specificity can be changed by mutation or pH change (read-in and read-out of the information). 3) Semiconductors and electronic capabilities can be achieved: we show that nanocellulose is rendered electronic by iodine treatment replacing silicon including microstructures. Nanocellulose semiconductor properties are measured, and the resulting potential including single-electron transistors (SET) and their properties are modeled. Electric current can also be transported by DNA through G-quadruplex DNA molecules; these as well as classical silicon semiconductors can easily be integrated into the nanocellulose composite. 4) To elaborate upon miniaturization and integration for a smart nanocellulose chip device, we demonstrate pH-sensitive dyes in nanocellulose, nanopore creation, and kinase micropatterning on bacterial membranes as well as digital PCR micro-wells. Future application potential includes nano-3D printing and fast molecular processors (e.g., SETs) integrated with DNA storage and conventional electronics. This would also lead to environment-friendly nanocellulose chips for information processing as well as smart nanocellulose composites for biomedical applications and nano-factories.
KW  - nanocellulose
KW  - DNA storage
KW  - light-gated proteins
KW  - single-electron transistors
KW  - protein chip
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-283033
SN  - 2296-4185
VL  - 10
ER  -