Next-generation physiology approaches to study microbiome function at single cell level

R Hatzenpichler, V Krukenberg, RL Spietz… - Nature Reviews …, 2020 - nature.com
The function of cells in their native habitat often cannot be reliably predicted from genomic
data or from physiology studies of isolates. Traditional experimental approaches to study the …

Learning and memory formation in zebrafish: Protein dynamics and molecular tools

K Reemst, H Shahin, OD Shahar - Frontiers in Cell and …, 2023 - frontiersin.org
Research on learning and memory formation at the level of neural networks, as well as at
the molecular level, is challenging due to the immense complexity of the brain. The zebrafish …

Lipidated variants of the antimicrobial peptide nisin produced via incorporation of methionine analogs for click chemistry show improved bioactivity

L Guo, C Wang, J Broos, OP Kuipers - Journal of Biological Chemistry, 2023 - ASBMB
The increase in antibiotic resistance calls for accelerated molecular engineering strategies
to diversify natural products for drug discovery. The incorporation of non-canonical amino …

Metabolic implications of using BioOrthogonal Non-Canonical Amino Acid Tagging (BONCAT) for tracking protein synthesis

KF Steward, B Eilers, B Tripet, A Fuchs… - Frontiers in …, 2020 - frontiersin.org
BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT) is a powerful tool for tracking
protein synthesis on the level of single cells within communities and whole organisms. A …

Experimental lipophilicity scale for coded and noncoded amino acid residues

V Kubyshkin - Organic & Biomolecular Chemistry, 2021 - pubs.rsc.org
Among other features, the polarity of amino acid residues is the key parameter for
understanding their role in proteins. The wide occurrence of protein modifications in nature …

Azidohomoalanine: A minimally invasive, versatile, and sensitive infrared label in proteins to study ligand binding

C Zanobini, O Bozovic, B Jankovic… - The Journal of …, 2018 - ACS Publications
The noncanonical amino acid azidohomoalanine (Aha) is known to be an environment-
sensitive infrared probe for the site-specific investigation of protein structure and dynamics …

Master equation model to predict energy transport pathways in proteins

L Valiño Borau, A Gulzar, G Stock - The Journal of chemical physics, 2020 - pubs.aip.org
Recent time-resolved experiments and accompanying molecular dynamics simulations
allow us to monitor the flow of vibrational energy in biomolecules. As a simple means to …

[HTML][HTML] De novo proteomic methods for examining the molecular mechanisms underpinning long-term memory

HT Evans, D Blackmore, J Götz, LG Bodea - Brain Research Bulletin, 2021 - Elsevier
Memory formation is a fundamental function of the nervous system that enables the
experience-based adaptation of behaviour. The formation, recall and updating of long-term …

Energy transport pathways in proteins: a non-equilibrium molecular dynamics simulation study

A Gulzar, L Valiño Borau, S Buchenberg… - Journal of chemical …, 2019 - ACS Publications
To facilitate the observation of biomolecular energy transport in real time and with single-
residue resolution, recent experiments by Baumann et al.(Angew. Chem. Int. Ed. 2019, 58 …

Spatially resolved correlative microscopy and microbial identification reveal dynamic depth‐and mineral‐dependent anabolic activity in salt marsh sediment

J Marlow, R Spietz, KY Kim, M Ellisman… - Environmental …, 2021 - Wiley Online Library
Coastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to
investigate the community structure of complex microbial communities. Here, we clarify …