Search results for "Biophysics"
showing 10 items of 3515 documents
Orientation and Dynamics of Peptides in Membranes Calculated from 2H-NMR Data
2009
Solid-state (2)H-NMR is routinely used to determine the alignment of membrane-bound peptides. Here we demonstrate that it can also provide a quantitative measure of the fluctuations around the distinct molecular axes. Using several dynamic models with increasing complexity, we reanalyzed published (2)H-NMR data on two representative alpha-helical peptides: 1), the amphiphilic antimicrobial peptide PGLa, which permeabilizes membranes by going from a monomeric surface-bound to a dimeric tilted state and finally inserting as an oligomeric pore; and 2), the hydrophobic WALP23, which is a typical transmembrane segment, although previous analysis had yielded helix tilt angles much smaller than ex…
The dynamic orientation of membrane-bound peptides: bridging simulations and experiments.
2007
AbstractThe structural organization in a peptide/membrane supramolecular complex is best described by knowledge of the peptide orientation plus its time-dependent and spatial fluctuations. The static orientation, defined by the peptide tilt and a rotation about its molecular axis, is accessible through a number of spectroscopic methods. However, peptide dynamics, although relevant to understand the functionality of these systems, remains largely unexplored. Here, we describe the orientation and dynamics of Trp-flanked and Lys-flanked hydrophobic peptides in a lipid bilayer from molecular dynamics simulations. A novel view is revealed, where collective nontrivial distributions of time-evolvi…
Self-Assembling of Peptide/Membrane Complexes by Atomistic Molecular Dynamics Simulations
2007
Abstract Model biological membranes consisting of peptide/lipid-bilayer complexes can nowadays be studied by classical molecular dynamics (MD) simulations at atomic detail. In most cases, the simulation starts with an assumed state of a peptide in a preformed bilayer, from which equilibrium configurations are difficult to obtain due to a relatively slow molecular diffusion. As an alternative, we propose an extension of reported work on the self-organization of unordered lipids into bilayers, consisting of including a peptide molecule in the initial random configuration to obtain a membrane-bound peptide simultaneous to the formation of the lipid bilayer. This strategy takes advantage of the…
Modulation Theory of Adhesion: Role of the Ectoenzymes Glycosidase and Glycosyltransferase
1986
It is amazing, but still plausible, that in all animal systems hitherto studied there is only one basic principle by which cell-cell recognition occurs. From sponges to higher eukaryotes there is only a small number of cell adhesion molecules which are involved in cell-cell adhesion. Specificities and histogenetic patterning are achieved by modulating processes acting on cell adhesion molecules. In sponges (secondary aggregation system) and in other eukaryotes, the activity and function of cell adhesion molecules are assumed to be modulated by enzymatic processes (glycosylation and deglycosylation). Strong evidence from experiments with sponges is available which indicates that modulation c…
Chain Stiffness of Elastin-Like Polypeptides
2010
The hydrodynamic radii of a series of genetically engineered monodisperse elastin like polypeptides (ELP) was determined by dynamic light scattering in aqueous solution as function of molar mass. Utilizing the known theoretical expression for the hydrodynamic radius of wormlike chains, the Kuhn statistical segment length was determined to be lk = 2.1 nm, assuming that the length of the peptide repeat unit was b = 0.365 nm, a value derived for a coiled conformation of ELP. The resulting chain stiffness is significantly larger than previously reported by force-distance curve analysis (lk < 0.4 nm). The possible occurrence of superstructures, such as hairpins or helices, would reduce the conto…
The uptake of N-(2-hydroxypropyl)-methacrylamide based homo, random and block copolymers by human multi-drug resistant breast adenocarcinoma cells
2009
A series of well-defined, fluorescently labelled homopolymers, random and block copolymers based on N-(2-hydroxypropyl)-methacrylamide were prepared by reversible addition–fragmentation chain transfer polymerization (RAFT polymerization). The polydispersity indexes for all polymers were in the range of 1.2–1.3 and the number average of the molar mass (Mn) for each polymer was set to be in the range of 15–30 kDa. The cellular uptake of these polymers was investigated in the human multi-drug resistant breast adenocarcinoma cell line MCF7/ADR. The uptake greatly depended on the polymer molecular mass and structure. Specifically, smaller polymers (approx. 15 kDa) were taken up by the cells at m…
Photoaffinity cross-linking of F1ATPase from the thermophilic bacterium PS3 by 3′-arylazido-β-alanyl-2-azido ATP
1989
AbstractThe photoactivatable bifunctional 3′-arylazido-β-alanyl-2-azido ATP (2,3′-DiN3ATP) has been applied to study the localization of the nucleotide-binding sites of coupling factor 1 (F1ATPase, TF1) from the thermophilic bacterium PS3 by photoaffinity cross-linking. UV irradiation of TF1 in the presence of 2,3′-DiN3ATP results in the nucleotide-dependent formation of various higher molecular mass cross-links formed by two, three or even four α- and/or β-subunits. The differences observed upon photoaffinity cross-linking by the bifunctional 2-azido ATP or 8-azido ATP analog are discussed. They are probably due to the varied maximal distance between both azido groups, or to the different …
Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET.
2021
Cellular function depends on the correct folding of proteins inside the cell. Heat-shock proteins 70 (Hsp70s), being among the first molecular chaperones binding to nascently translated proteins, aid in protein folding and transport. They undergo large, coordinated intra- and interdomain structural rearrangements mediated by allosteric interactions. Here, we applied a three-color single-molecule Forster resonance energy transfer (FRET) combined with three-color photon distribution analysis to compare the conformational cycle of the Hsp70 chaperones DnaK, Ssc1, and BiP. By capturing three distances simultaneously, we can identify coordinated structural changes during the functional cycle. Be…
Design of bioactive and structurally well-defined peptides from conformationally restricted libraries
2004
Libraries of peptides and proteins can be categorized according to the function of their origin in gene- and synthetic-based libraries. Both kinds of libraries have the potential to generate the same grade of molecular diversity, although the limits imposed by the synthetic methods have been lately a matter of discussion. However, the use of synthetic strategies allows incorporation of non-natural amino acids. The development of canfonnallonally restricted synthetic peptide libraries can be considered as a point of convergence of the two methodologies. In these libraries the diversity is grafted into scaffolds that are defined by stable secondary structural motifs, and the deconvolution pro…