Results 41 to 50 of about 3,678,372 (337)
Protein Allostery and Conformational Dynamics [PDF]
Chemical Reviews, 2016 The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding
Jingjing, Guo, Huan-Xiang, Zhou
openaire +2 more sources
Protein dynamics and conformational selection in bidirectional signal transduction
BMC Biology, 2012 Protein conformational dynamics simultaneously allow promiscuity and specificity in binding. The multiple conformations of the free EphA4 ligand-binding domain observed in two new EphA4 crystal structures provide a unique insight into the conformational ...
Nussinov Ruth, Ma Buyong
doaj +1 more source
bioRxiv, 2020 The SARS-CoV-2 spike (S) protein is the target of vaccine design efforts to end the COVID-19 pandemic. Despite a low mutation rate, isolates with the D614G substitution in the S protein appeared early during the pandemic, and are now the dominant form ...
S. Gobeil +11 more
semanticscholar +1 more source
Efficient and Accurate Modeling of Conformational Transitions in Proteins: The Case of c-Src Kinase [PDF]
, 2018 The theoretical computational modeling of large conformational transitions occurring in biomolecules still represents a challenge. Here, we present an accurate "in silico" description of the activation and deactivation mechanisms of human c-Src kinases ...
Alexandra G. Trandafir +4 more
core +2 more sources
Mapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers
Nature Communications, 2022 Quantitative characterization of kinase conformational dynamics remains challenging. Here, the authors show that protein nanopore tweezers allow analyzing the conformational energy landscape and ligand binding of the Abl kinase domain.
Fanjun Li +4 more
doaj +1 more source
bioRxiv, 2020 Single-molecule FRET experiments with human A2A adenosine receptor in its apo and agonist-bound states in lipid nanodiscs provide insights into its conformational dynamics and activation. The complex pharmacology of G-protein-coupled receptors (GPCRs) is
I. Maslov +18 more
semanticscholar +1 more source
Faithful Estimation of Dynamics Parameters from CPMG Relaxation Dispersion Measurements [PDF]
, 2006 This work examines the robustness of fitting of parameters describing conformational exchange (kex, pa/b, and Δω) processes from CPMG relaxation dispersion data.
Grey, Michael J. +3 more
core +2 more sources
Models of Conformational Dynamics [PDF]
, 1989 Discrete master equations can be obtained from diffusion-Smoluchowski equation in the presence of large barriers separating the potential minima, the treatment being equivalent to the derivation of the Kramers transition rates in the overdamped regime. The one-dimensional problem is considered as a test case to illustrate the projection procedure onto ...
MORO, GIORGIO +3 more
openaire +2 more sources
Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. [PDF]
, 2010 A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin ...
Abel, Barrett L +5 more
core +2 more sources
Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations. [PDF]
PLoS ONE, 2015 Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis.
Federico Fogolari +8 more
doaj +1 more source