Search results for "Protein dynamic"
showing 10 items of 82 documents
Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates
2013
Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We sho…
The protein dynamical transition does not require the protein polypeptide chain
2011
We give experimental evidence that the main features of protein dynamics revealed by neutron scattering, i.e., the “protein dynamical transition” and the “boson peak”, do not need the protein polypeptide chain. We show that a rapid increase of hydrogen atoms fluctuations at about 220 K, analogous to the one observed in hydrated myoglobin powders, is also observed in a hydrated amino acids mixture with the chemical composition of myoglobin but lacking the polypeptide chain; in agreement with the protein behavior, the transition is abolished in the dry mixture. Further, an excess of low-frequency vibrational modes around 3 meV, typically observed in protein powders, is also observed in our mi…
Protein/Hydration Water Dynamics in Hard Confinement: Dielectric Relaxations and Picoseconds Hydrogen Fluctuations
2011
In this review we report on some experimental studies on the dynamics of Myoglobin in a confined geometry, obtained by encapsulation in a porous silica matrix, at low hydration levels. After formation through the solgel method, the samples were left aging/drying in order to reach a condition where only one or two water layers surround the proteins. In order to put in evidence the specific effect of confinement in the silica host, we compared this system with another one (i.e. hydrated powder) where proteins are confined by other proteins. Using elastic neutron scattering we investigate the temperature dependence of the mean square displacements of non-exchangeable hydrogen atoms of sol-gel …
Hemoglobin dynamics probed by picosecond wide-angle x-ray scattering
2008
THE PHYSICAL ORIGIN OF PROTEIN DYNAMICAL TRANSITION: A LIQUID-LIQUID TRANSITION IN HYDRATION WATER?
2015
In this thesis I study, by means of neutron scattering, calorimetry, and dielectric spectroscopy, the physical origin of protein dynamical transition (PDT) which is usually observed at ~230 K in protein hydrated powders and is deemed necessary for protein function. Measurements reported in this thesis have been performed on hydrated powders of Myoglobin. The combined use of different experimental techniques gives a coherent description of the PDT and reveals a connection with a liquid-liquid crossover occurring in the protein hydration water at about the same temperature. In order to deepen our understanding of this connection and to obtain a direct experimental evidence of the existence of…
On dynamics of parvoviral replication protein NS1
2010
Hydration dependence of myoglobin dynamics studied with elastic neutron scattering, differential scanning calorimetry and broadband dielectric spectr…
2014
In this work we present a thorough investigation of the hydration dependence of myoglobin dynamics. The study is performed on D2O-hydrated protein powders in the hydration range 0<h<0.5 (h≡gr[D2O]/gr[protein]) and in the temperature range 20-300K. The protein equilibrium fluctuations are investigated with Elastic Neutron Scattering using the spectrometer IN13 at ILL (Grenoble), while the relaxations of the protein + hydration water system are investigated with Broadband Dielectric Spectroscopy; finally, Differential Scanning Calorimetry is used to obtain a thermodynamic description of the system. The effect of increasing hydration is to speed up the relaxations of the myoglobin + hydration …