Conformational dynamics and enzyme evolution

D Petrović, VA Risso, SCL Kamerlin… - Journal of the …, 2018 - royalsocietypublishing.org
Enzymes are dynamic entities, and their dynamic properties are clearly linked to their
biological function. It follows that dynamics ought to play an essential role in enzyme …

Biophysics of protein evolution and evolutionary protein biophysics

T Sikosek, HS Chan - Journal of The Royal Society …, 2014 - royalsocietypublishing.org
The study of molecular evolution at the level of protein-coding genes often entails comparing
large datasets of sequences to infer their evolutionary relationships. Despite the importance …

[HTML][HTML] Conservation of protein structure over four billion years

A Ingles-Prieto, B Ibarra-Molero, A Delgado-Delgado… - Structure, 2013 - cell.com
Little is known about the evolution of protein structures and the degree of protein structure
conservation over planetary time scales. Here, we report the X-ray crystal structures of seven …

On the universe of protein folds

R Kolodny, L Pereyaslavets… - Annual review of …, 2013 - annualreviews.org
In the fifty years since the first atomic structure of a protein was revealed, tens of thousands
of additional structures have been solved. Like all objects in biology, proteins structures …

Simulations of a protein fold switch reveal crowding-induced population shifts driven by disordered regions

S Bazmi, B Seifi, S Wallin - Communications Chemistry, 2023 - nature.com
Macromolecular crowding effects on globular proteins, which usually adopt a single stable
fold, have been widely studied. However, little is known about crowding effects on fold …

Exploring the sequence fitness landscape of a bridge between protein folds

P Tian, RB Best - PLoS computational biology, 2020 - journals.plos.org
Most foldable protein sequences adopt only a single native fold. Recent protein design
studies have, however, created protein sequences which fold into different structures apon …

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

M Knott, RB Best - The Journal of chemical physics, 2014 - pubs.aip.org
Many proteins undergo a conformational transition upon binding to their cognate binding
partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which …

Metamorphic proteins: the Janus proteins of structural biology

K Madhurima, B Nandi, A Sekhar - Open biology, 2021 - royalsocietypublishing.org
The structural paradigm that the sequence of a protein encodes for a unique three-
dimensional native fold does not acknowledge the intrinsic plasticity encapsulated in …

Emergence of de novo proteins from 'dark genomic matter' by 'grow slow and moult'

E Bornberg-Bauer, J Schmitz… - Biochemical Society …, 2015 - portlandpress.com
Proteins are the workhorses of the cell and, over billions of years, they have evolved an
amazing plethora of extremely diverse and versatile structures with equally diverse …

The rise and fall of TRP-N, an ancient family of mechanogated ion channels, in metazoa

A Schüler, G Schmitz, A Reft, S Özbek… - Genome biology and …, 2015 - academic.oup.com
Mechanoreception, the sensing of mechanical forces, is an ancient means of orientation and
communication and tightly linked to the evolution of motile animals. In flies, the transient …