1,721,458 research outputs found
Unfolding proteins by external forces and temperature: The importance of topology and energetics
No full textUnfolding of proteins by forced stretching with atomic force microscopy or laser tweezer experiments complements more classical techniques using chemical denaturants or temperature. Forced unfolding is of particular interest for proteins that are under mechanical stress in their biological function. For β-sandwich proteins (a fibronectin type III and an immunoglobulin domain), both of which appear in the muscle protein titin, the results of stretching simulations show important differences from temperature-induced unfolding, but there are common features that point to the existence of folding cores. Intermediates detected by comparing unfolding with a biasing perturbation and a constant pulling force are not evident in temperature-induced unfolding. For an α-helical domain (α-spectrin), which forms part of the cytoskeleton, there is little commonality in the pathways from unfolding induced by stretching and temperature. Comparison of the forced unfolding of the two β-sandwich proteins and two α-helical proteins (the α-spectrin domain and an acyl-coenzyme A-binding protein) highlights important differences within and between protein classes that are related to the folding topologies and the relative stability of the various structural elements
Liver. III: Gadolinium-based hepatobiliary contrast agents (Gd-EOB-DTPA and Gd-BOPTA/Dimeg)
No full text: Gd-EOB-DTPA and Gd-BOPTA/Dimeg are two paramagnetic contrast agents that are unlikely ECF contrast agents but that are selectively taken up by hepatocytes and yield a selective enhancement of the liver parenchyma on T1-weighted images. Gd-EOB-DTPA yields hepatocellular specific uptake within the biliary excretion rate of 50% of the injected dose. Gd-BOPTA/Dimeg is taken up by hepatocytes in a small portion (2%-4%); however, its high relaxivity provides a significant and sustained increase of signal intensity of the normal liver. Both compounds have demonstrated a safe pharmacologic and toxicologic profile on preclinical evaluation and phase I clinical trials. Preliminary results demonstrate that these contrast agents may improve the MR imaging capability to detect focal liver lesions, with a dramatic and selective increase of liver signal-to-noise ratio and lesion-liver contrast-to-noise ratio. The wide imaging window, allowed by the sustained enhancement achieved after injection also provides flexibility in selecting an imaging sequence
Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulation at high pressure
No full textConstant pressure and temperature molecular dynamics techniques have been employed to investigate the changes in structure and volumes of two globular proteins, superoxide dismutase and lysozyme, under pressure. Compression (the relative changes in the proteins' volumes), computed with the Voronoi technique, is closely related with the so-called protein intrinsic compressibility, estimated by sound velocity measurements. In particular, compression computed with Voronoi volumes predicts, in agreement with experimental estimates, a negative bound water contribution to the apparent protein compression. While the use of van der Waals and molecular volumes underestimates the intrinsic compressibilities of proteins, Voronoi volumes produce results closer to experimental estimates. Remarkably, for two globular proteins of very different secondary structures, we compute identical (within statistical error) protein intrinsic compressions, as predicted by recent experimental studies. Changes in the protein interatomic distances under compression are also investigated. It is found that, on average, short distances compress less than longer ones. This nonuniform contraction underlines the peculiar nature of the structural changes due to pressure in contrast with temperature effects, which instead produce spatially uniform changes in proteins. The structural effects observed in the simulations at high pressure can explain protein compressibility measurements carried out by fluorimetric and hole burning techniques. Finally, the calculation of the proteins static structure factor shows significant shifts in the peaks at short wavenumber as pressure changes. These effects might provide an alternative way to obtain information concerning compressibilities of selected protein regions
Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
No full textTitin, an important constituent of vertebrate muscles, is a protein of the order of a micrometer in length in the folded state. Atomic force microscopy and laser tweezer experiments have been used to stretch titin molecules to more than ten times their folded lengths. To explain the observed relation between force and extension, it has been suggested that the immunoglobulin and fibronectin domains unfold one at a time in an all-or-none fashion. We use molecular dynamics simulations to study the forced unfolding of two different fibronectin type 3 domains (the ninth, 9Fn3, and the tenth, 10Fn3, from human fibronectin) and of their heterodimer of known structure. An external biasing potential on the N to C distance is employed and the protein is treated in the polar hydrogen representation with an implicit solvation model. The latter provides an adiabatic solvent response, which is important for the nanosecond unfolding simulation method used here. A series of simulations is performed for each system to obtain meaningful results. The two different fibronectin domains are shown to unfold in the same way along two possible pathways. These involve the partial separation of the 'P-sandwich', an essential structural element, and the unfolding of the individual sheets in a stepwise fashion. The biasing potential results are confirmed by constant force unfolding simulations. For the two connected domains, there is complete unfolding of one domain (9Fn3) before major unfolding of the second domain (10Fn3). Comparison of different models for the potential energy function demonstrates that the dominant cohesive element in both proteins is due to the attractive van der Waals interactions; electrostatic interactions play a structural role but appear to make only a small contribution to the stabilization of the domains, in agreement with other studies of β-sheet stability. The unfolding forces found in the simulations are of the order of those observed experimentally, even though the speed of the former is more than six orders of magnitude greater than that used in the latter
Helical Polyampholyte Sequences Have Unique Thermodynamic Properties
No full textHelices are the most common structural pattern observed in structured proteins. Polypeptide sequences that form helices in isolation have been identified and extensively studied. These are generally rich in alanine, the amino acid with strongest helical propensity. Insertion of charged or polar amino acids has been shown to be necessary to make alanine-rich peptides soluble and sometimes even increase the helicity of the peptides. More recently sequences that contain mostly charged residues (E-R/K rich) have been found in naturally occurring proteins that are highly helical, soluble, and extended regardless their length. Artificial sequences composed mostly or exclusively of charged amino acids have been designed that are also highly helical, depending on the specific pattern of oppositely charged residues. Here we explore the thermodynamic properties of a number of 16-residue long peptides with varying helical propensity by performing equilibrium simulations over a broad range of temperatures. We observe quantitative differences in the peptides' helical propensities that can be related to qualitative differences in the free energy landscape, depending on the ampholytic patterns in the sequence. The results provide hints on how the specific physical properties of naturally occurring long sequences with similar patterns of charged residues may relate to their biological function
VACANCY MIGRATION RATES BY MOLECULAR-DYNAMICS WITH CONSTRAINTS
No full textRate constants for vacancy migration in a Lennard-Jones crystal are evaluated within the frame of the reactive flux correlation function formalism by molecular dynamics simulation. In our calculation a key role is played by a holonomic constraint acting on the reaction coordinate. The definition of a suitable reaction coordinate is a subtle matter as becomes evident when using our techniques. We show bow the ambiguities in the definition of the reaction coordinate can be circumvented. Our results are two orders of magnitude more precise than previous 'exact' calculations
Molecular Dynamics Simulations to Study Protein Folding and Unfolding
No full textProteins in solution fold in time scales ranging from microseconds to seconds. A computational approach to folding that should work, in principle, is to use an atom-based model for the potential energy (force field) and to solve the time- discretized Newton equation of motion (molecular dynamics, MD [1]) from a dena- tured conformer to the native state in the presence of the appropriate solvent
Conflitti, paci e vendette nell'Italia comunale
No full textConflitti, paci e vendette nell'Italia comunale Seminario di studi organizzato dal Dottorato di ricerca in Storia medievale in collaborazione con il Centro di Studi sulla Civiltà ComunaleDipartimento di Studi Storici e Geografici Università degli Studi di FirenzeFirenze, 26 gennaio 2005Programma Aula 21 di Palazzo Fenzi Via S. Gallo, 10ore 9:30 Federico RomeroDirettore del Dipartimento di Studi storici e geograficiJean-Claude Maire VigueurCoordinatore del Dottorato di ricerca in Storia ..
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