Macromolecular crowding is more than hard-core repulsions

SL Speer, CJ Stewart, L Sapir… - Annual Review of …, 2022 - annualreviews.org
Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We
review the experimental evidence that crowding affects the equilibrium thermodynamics of …

Surface proteins of gram-positive bacteria and mechanisms of their targeting to the cell wall envelope

WW Navarre, O Schneewind - Microbiology and molecular biology …, 1999 - journals.asm.org
The cell wall envelope of gram-positive bacteria is a macromolecular, exoskeletal organelle
that is assembled and turned over at designated sites. The cell wall also functions as a …

A protein-tagging system for signal amplification in gene expression and fluorescence imaging

ME Tanenbaum, LA Gilbert, LS Qi, JS Weissman… - Cell, 2014 - cell.com
Signals in many biological processes can be amplified by recruiting multiple copies of
regulatory proteins to a site of action. Harnessing this principle, we have developed a …

How sugars protect dry protein structure

JA Brom, RG Petrikis, GJ Pielak - Biochemistry, 2023 - ACS Publications
Extremotolerant organisms and industry exploit sugars as desiccation protectants, with
trehalose being widely used by both. How sugars, in general, and the hydrolytically stable …

A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain

CA Olson, NC Wu, R Sun - Current biology, 2014 - cell.com
Background Nonadditivity in fitness effects from two or more mutations, termed epistasis, can
result in compensation of deleterious mutations or negation of beneficial mutations. Recent …

Engineering shape memory and morphing protein hydrogels based on protein unfolding and folding

Q Bian, L Fu, H Li - Nature communications, 2022 - nature.com
Engineering shape memory/morphing materials have achieved considerable progress in
polymer-based systems with broad potential applications. However, engineering protein …

Combining an elastic network with a coarse-grained molecular force field: structure, dynamics, and intermolecular recognition

X Periole, M Cavalli, SJ Marrink… - Journal of chemical …, 2009 - ACS Publications
Structure-based and physics-based coarse-grained molecular force fields have become
attractive approaches to gain mechanistic insight into the function of large biomolecular …

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

KT Simons, C Kooperberg, E Huang, D Baker - Journal of molecular biology, 1997 - Elsevier
We explore the ability of a simple simulated annealing procedure to assemble native-like
structures from fragments of unrelated protein structures with similar local sequences using …

Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling

SG Hyberts, AG Milbradt, AB Wagner… - Journal of biomolecular …, 2012 - Springer
The fast Fourier transformation has been the gold standard for transforming data from time to
frequency domain in many spectroscopic methods, including NMR. While reliable, it has as …

Inferring protein 3D structure from deep mutation scans

NJ Rollins, KP Brock, FJ Poelwijk, MA Stiffler… - Nature …, 2019 - nature.com
We describe an experimental method of three-dimensional (3D) structure determination that
exploits the increasing ease of high-throughput mutational scans. Inspired by the success of …