Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
Intrinsically disordered proteins from A to Z
VN Uversky - The international journal of biochemistry & cell biology, 2011 - Elsevier
The ideas that proteins might possess specific functions without being uniquely folded into
rigid 3D-structures and that these floppy polypeptides might constitute a noticeable part of …
rigid 3D-structures and that these floppy polypeptides might constitute a noticeable part of …
Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables
Abstract Motivation: Intrinsically disordered proteins (IDPs) represent a significant fraction of
the human proteome. The classical structure function paradigm that has successfully …
the human proteome. The classical structure function paradigm that has successfully …
Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data
Protein dynamics on the atomic level and on the microsecond timescale has recently
become accessible from both computation and experiment. To validate molecular dynamics …
become accessible from both computation and experiment. To validate molecular dynamics …
Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings
Intrinsically disordered proteins (IDPs) inhabit a conformational landscape that is too
complex to be described by classical structural biology, posing an entirely new set of …
complex to be described by classical structural biology, posing an entirely new set of …
Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition
RB Fenwick, S Esteban-Martín, B Richter… - Journal of the …, 2011 - ACS Publications
Long-range correlated motions in proteins are candidate mechanisms for processes that
require information transfer across protein structures, such as allostery and signal …
require information transfer across protein structures, such as allostery and signal …
Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description
F Spyrakis, CN Cavasotto - Archives of biochemistry and biophysics, 2015 - Elsevier
Abstract Structure-based virtual screening is currently an established tool in drug lead
discovery projects. Although in the last years the field saw an impressive progress in terms …
discovery projects. Although in the last years the field saw an impressive progress in terms …
Predicting protein flexibility through the prediction of local structures
A Bornot, C Etchebest… - … : Structure, Function, and …, 2011 - Wiley Online Library
Protein structures are valuable tools for understanding protein function. However, protein
dynamics is also considered a key element in protein function. Therefore, in addition to …
dynamics is also considered a key element in protein function. Therefore, in addition to …
A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed
L Salmon, G Bascom, I Andricioaei… - Journal of the …, 2013 - ACS Publications
The ability to modulate alignment and measure multiple independent sets of NMR residual
dipolar couplings (RDCs) has made it possible to characterize internal motions in proteins at …
dipolar couplings (RDCs) has made it possible to characterize internal motions in proteins at …
Emerging methods for ensemble-based virtual screening
Ensemble based virtual screening refers to the use of conformational ensembles from crystal
structures, NMR studies or molecular dynamics simulations. It has gained greater …
structures, NMR studies or molecular dynamics simulations. It has gained greater …