Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

C Micheletti - Physics of life reviews, 2013 - Elsevier
The growing interest for comparing protein internal dynamics owes much to the realisation
that protein function can be accompanied or assisted by structural fluctuations and …

Femtosecond crystallography with ultrabright electrons and x-rays: Capturing chemistry in action

RJD Miller - Science, 2014 - science.org
With the recent advances in ultrabright electron and x-ray sources, it is now possible to
extend crystallography to the femtosecond time domain to literally light up atomic motions …

The role of conformational dynamics and allostery in modulating protein evolution

P Campitelli, T Modi, S Kumar… - Annual review of …, 2020 - annualreviews.org
Advances in sequencing techniques and statistical methods have made it possible not only
to predict sequences of ancestral proteins but also to identify thousands of mutations in the …

The interface of protein structure, protein biophysics, and molecular evolution

DA Liberles, SA Teichmann, I Bahar, U Bastolla… - Protein …, 2012 - Wiley Online Library
Abstract The interface of protein structural biology, protein biophysics, molecular evolution,
and molecular population genetics forms the foundations for a mechanistic understanding of …

Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme

T Zou, VA Risso, JA Gavira… - Molecular biology …, 2015 - academic.oup.com
β-lactamases are produced by many modern bacteria as a mechanism of resistance toward
β-lactam antibiotics, the most common antibiotics in use. β-lactamases, however, are ancient …

Mapping atomic motions with ultrabright electrons: The chemists' Gedanken experiment enters the lab frame

RJD Miller - Annual review of physical chemistry, 2014 - annualreviews.org
This review documents the development of high–bunch charge electron pulses with
sufficient combined spatiotemporal resolution and intensity to literally light up atomic …

Measuring and comparing structural fluctuation patterns in large protein datasets

E Fuglebakk, J Echave, N Reuter - Bioinformatics, 2012 - academic.oup.com
Motivation: The function of a protein depends not only on its structure but also on its
dynamics. This is at the basis of a large body of experimental and theoretical work on protein …

Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis

A Ramanathan, PK Agarwal - PLoS biology, 2011 - journals.plos.org
Proteins are intrinsically flexible molecules. The role of internal motions in a protein's
designated function is widely debated. The role of protein structure in enzyme catalysis is …

Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications

Z Liang, GM Verkhivker, G Hu - Briefings in bioinformatics, 2020 - academic.oup.com
Proteins are dynamical entities that undergo a plethora of conformational changes,
accomplishing their biological functions. Molecular dynamics simulation and normal mode …

Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure

JA Marsh, SA Teichmann - BioEssays, 2014 - Wiley Online Library
Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of
conformational fluctuations, and individual protein chains can assemble into complexes …