Lessons from the lysozyme of phage T4

WA Baase, L Liu, DE Tronrud, BW Matthews - Protein Science, 2010 - Wiley Online Library
An overview is presented of some of the major insights that have come from studies of the
structure, stability, and folding of T4 phage lysozyme. A major purpose of this review is to …

Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets

DR Davies, AD Gelinas, C Zhang… - Proceedings of the …, 2012 - National Acad Sciences
Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful
method of identifying high-affinity ligands for a broad range of molecular targets …

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity

T Paramo, A East, D Garzón… - Journal of chemical …, 2014 - ACS Publications
Protein cavities and tunnels are critical in determining phenomena such as ligand binding,
molecular transport, and enzyme catalysis. Molecular dynamics (MD) simulations enable the …

High-quality thermodynamic data on the stability changes of proteins upon single-site mutations

F Pucci, R Bourgeas, M Rooman - Journal of Physical and Chemical …, 2016 - pubs.aip.org
We have set up and manually curated a dataset containing experimental information on the
impact of amino acid substitutions in a protein on its thermal stability. It consists of a …

Pressure as a tool to study protein-unfolding/refolding processes: the case of ribonuclease A

M Ribo, J Font, A Benito, J Torrent, R Lange… - … et Biophysica Acta (BBA …, 2006 - Elsevier
This paper gives an overview of the application of high-pressure to study the
folding/unfolding processes of proteins using Ribonuclease A as a model protein. A …

Fluorescence “turn-off/turn-on” biosensing of metal ions by gold nanoclusters, folic acid and reduced graphene oxide

XY Wong, D Quesada-González, S Manickam… - Analytica Chimica …, 2021 - Elsevier
Metal ions homeostasis plays an important role in biological processes. The ability to detect
the concentration of metal ions in biological fluids is often challenged by the obvious …

Total synthesis by modern chemical ligation methods and high resolution (1.1 Å) X‐ray structure of ribonuclease A

DJ Boerema, VA Tereshko, SBH Kent - Peptide Science, 2008 - Wiley Online Library
The total chemical synthesis of RNase A using modern chemical ligation methods is
described, illustrating the significant advances that have been made in chemical protein …

Conservation of flexible residue clusters among structural and functional enzyme homologues

D Gagné, LA Charest, S Morin, EL Kovrigin… - Journal Of Biological …, 2012 - ASBMB
Conformational flexibility between structural ensembles is an essential component of
enzyme function. Although the broad dynamical landscape of proteins is known to promote a …

Size-dependent relationships between protein stability and thermal unfolding temperature have important implications for analysis of protein energetics and high …

MD Watson, J Monroe, DP Raleigh - The Journal of Physical …, 2017 - ACS Publications
Changes in protein stability are commonly reported as changes in the melting temperature,
Δ TM, or as changes in unfolding free energy at a particular temperature, ΔΔ G°. Using data …

Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily

C Narayanan, D Gagné, KA Reynolds, N Doucet - Scientific reports, 2017 - nature.com
In this work, we applied the sequence-based statistical coupling analysis approach to
characterize conserved amino acid networks important for biochemical function in the …