Search results for "Protein dynamic"

Anharmonic activations in proteins and peptide model systems and their connection with supercooled water thermodynamics

2016

International audience; — Proteins, the nano-machines of living systems, are highly dynamic molecules. The timescale of functionally relevant motions spans over a very broad range, from femtoseconds to several seconds. In particular, the pico-to nanoseconds region is characterized by side-chain and backbone anharmonic fluctuations that are responsible for many biological tasks like ligand binding, substrate recognition and enzymatic activity. Neutron scattering on hydrated protein powders reveals two main activations of anharmonic dynamics, characterized by different onset temperature and amplitude. Here we review our work on synthetic polypeptides, native proteins, and single amino acids t…

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy

2014

Monitoring the dynamics of protonation and protein backbone conformation changes during the function of a protein is an essential step towards understanding its mechanism. Protonation and conformational changes affect the vibration pattern of amino acid side chains and of the peptide bond, respectively, both of which can be probed by infrared (IR) difference spectroscopy. For proteins whose function can be repetitively and reproducibly triggered by light, it is possible to obtain infrared difference spectra with (sub)microsecond resolution over a broad spectral range using the step-scan Fourier transform infrared technique. With -10(2)-10(3) repetitions of the photoreaction, the minimum num…

Protein and solvent dynamics of the water-soluble chlorophyll-binding protein (WSCP)

2015

This study presents quasielastic neutron scattering data of the water-soluble chlorophyll-binding protein (WSCP) and the corresponding buffer solution at room temperature. The contributions of protein and buffer solution to the overall scattering are carefully separated. Otherwise, the fast water dynamics dominating the buffer contribution is likely to mask the slow protein dynamics. In the case of WSCP, the protein scattering can be described by two contributions: i) internal protein dynamics represented by a diffusion in a sphere with an average radius of 2.7 u A and ii) global (Brownian) diffusion of the WSCP macromolecule with an upper limit for the translational diffusion coefficient o…

Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase

2013

Isotopic substitution (15N, 13C, 2H) of a catalytically compromised variant of Escherichia coli dihydrofolate reductase, EcDHFR-N23PP/S148A, has been used to investigate the effect of these mutations on catalysis. The reduction of the rate constant of the chemical step in the EcDHFR-N23PP/S148A catalyzed reaction is essentially a consequence of an increase of the quasi-classical free energy barrier and to a minor extent of an increased number of recrossing trajectories on the transition state dividing surface. Since the variant enzyme is less well set up to catalyze the reaction, a higher degree of active site reorganization is needed to reach the TS. Although millisecond active site motion…

THz spectroscopy studies on proteins: exploring collective modes of amyloid fibrils

2013

Quaternary structure dependence of kinetic hole burning and conformational substates interconversion in hemoglobin.

2003

Using a sol-gel encapsulation technique, we have prepared samples of CO saturated human adult hemoglobin locked in the R or T quaternary conformation. We report time-resolved spectra of these samples in the Soret region following flash photolysis, in the time interval ranging from 250 ns to 200 ms and in the temperature interval of 100-170 K. A suitable analysis of the measured difference spectra enables us to obtain the spectral contribution of deoxyHb and HbCO molecules as a function of time and/or of the fraction N(t) of deoxyHb molecules. In our experimental time window geminate CO rebinding to hemoglobin in the T quaternary conformation is about 2 orders of magnitude slower than to hem…

Protein dynamics: conformational disorder, vibrational coupling and anharmonicity in deoxy-hemoglobin and myoglobin.

1993

In this work we study the temperature dependence of the Soret band lineshape of deoxymyoglobin and deoxyhemoglobin, in the range 300-20 K. To fit the measured spectra we use an approach originally proposed by Champion and coworkers (Srajer et al. 1986; Srajer and Champion 1991). The band profile is modelled as a Voigt function that accounts for the coupling with low frequency vibrational modes, whereas the coupling with high frequency modes is responsible for the vibronic structure of the spectra. Moreover, owing to the position of the iron atom out of the mean heme plane, inhomogeneous broadening brings about a non-Gaussian distribution of 0-0 electronic transition frequencies. The reporte…

Dynamic properties of some β-chain mutant hemoglobins

1995

The thermal behavior of the Soret band relative to the carbonmonoxy derivatives of some beta-chain mutant hemoglobins is studied in the temperature range 300-10 K and compared to that of wild-type carbonmonoxy hemoglobin. The band profile at various temperatures is modeled as a Voigt function that accounts for homogeneous broadening and for the coupling with high- and low-frequency vibrational modes, while inhomogeneous broadening is taken into account with a gaussian distribution of purely electronic transition frequencies. The various contributions to the over-all bandwidth are singled out with this analysis and their temperature dependence, in turn, gives information on structural and dy…

Computational Modeling of Protein Dynamics in Eukaryotic Cells

2012

Proteins have important functions inside the cell, traveling diffusively or being actively transported to various cellular sites where their activity is needed. Protein motion in the cellular environment is therefore an important topic to understand. However, the cell provides a very complex environment for that motion, which poses problems especially for any modeling effort designed to interpret experimentally observed features. So as to gain a realistic picture of protein dynamics inside the cell, we have recently introduced advanced numerical methods for describing that dynamics [1]. The starting point is an accurate numerical duplicate of the cell determined by LSCM, which can be used a…

2015

Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N-terminal segment containing heavy isotopes (2H, 13C, 15N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C-terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N-terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C-terminal segment. QM/MM studies support the idea th…