Search results for "Folding"
showing 10 items of 330 documents
Acquisition of Structure-guiding and Structure-forming Properties during Maturation from the Pro-silicatein to the Silicatein Form
2012
Silicateins are the key enzymes involved in the enzymatic polycondensation of the inorganic scaffold of the skeletal elements of the siliceous sponges, the spicules. The gene encoding pro-silicatein is inserted into the pCold TF vector, comprising the gene for the bacterial trigger factor. This hybrid gene is expressed in Escherichia coli and the synthesized fusion protein is purified. The fusion protein is split into the single proteins with thrombin by cleavage of the linker sequence present between the two proteins. At 23 °C, the 87 kDa trigger factor-pro-silicatein fusion protein is cleaved to the 51 kDa trigger factor and the 35 kDa pro-silicatein. The cleavage process proceeds and res…
Atomic Structures of Two Novel Immunoglobulin-like Domain Pairs in the Actin Cross-linking Protein Filamin
2009
Filamins are actin filament cross-linking proteins composed of an N-terminal actin-binding domain and 24 immunoglobulin-like domains (IgFLNs). Filamins interact with numerous proteins, including the cytoplasmic domains of plasma membrane signaling and cell adhesion receptors. Thereby filamins mechanically and functionally link the cell membrane to the cytoskeleton. Most of the interactions have been mapped to the C-terminal IgFLNs 16–24. Similarly, as with the previously known compact domain pair of IgFLNa20–21, the two-domain fragments IgFLNa16–17 and IgFLNa18–19 were more compact in small angle x-ray scattering analysis than would be expected for two independent domains. Solution state NM…
Scaffolding patterns of dialogic exchange in toddler classrooms
2021
The present study investigates how often episodes of dialogic exchange can be identified in educator–toddler interactions during play and emerging academic activities, what kind of scaffolding strategies educators use during the episodes of dialogic exchange and, ultimately, what kind of scaffolding patterns of dialogic exchange can be identified based on educators' use of scaffolding strategies. Educator–child interactions were video-recorded in seven European countries, in two toddler classrooms in each country. The video recordings of emerging academic and play activities were transcribed and analysed, combining the principles of theory and a data-driven content analysis. First, 69 episo…
Clusterization and strong coupled-channels effects in deuteron interaction with $^9$Be nuclei
2019
Angular distributions of protons, deuterons, tritons and alpha particles emitted in the d + alt;supagt;9alt;/supagt;Be reaction at Ealt;subagt;labalt;/subagt;=19.5 and 35.0 MeV have been measured.a#13; The elastic scattering channel is analysed in the framework of both the Optical Model and the Coupled-Channel approach. a#13; The interaction potential of the alt;iagt;dalt;/iagt; + alt;supagt;9alt;/supagt;Be system is calculated in the framework of the Double-Folding model using the α+α+alt;iagt;nalt;/iagt; three-body wave function of the alt;supagt;9alt;/supagt;Be nucleus.a#13; The (alt;iagt;dalt;/iagt;,alt;iagt;palt;/iagt;) and (alt;iagt;dalt;/iagt;,alt;iagt;talt;/iagt;) one-nucleon-transf…
Flexibility of TTF. a theoretical study
1999
Abstract The folding of tetrathiafulvalene along the S···S axes has been investigated using highly-accurate quantum-chemical calculations. A very flat, two-fold potential is found for neutral TTF where minima correspond to boat conformations (θ ≈ 15–20 °). The flatness of the folding potential indicates that TTF is conformationally more flexible than usually thought.
Physics and biophysics of solvent induced forces: hydrophobic interactions and context-dependent hydration
1998
Solvent induced forces (SIFs) among solutes derive from solvent structural modification due to solutes, and consequent thermodynamic drive towards minimization of related free energy costs. The role of SIFs in biomolecular conformation and function is appreciated by observing that typical SIF values fall within the 20–200 pN interval, and that proteins are stable by only a few kcal mol–1 (1 kcal mol–1 corresponds to 70 pN A). Here we study SIFs, in systems of increasing complexity, using Molecular Dynamics (MD) simulations which give time- and space-resolved details on the biologically significant scale of single protein residues and sidechains. Of particular biological relevance among our …
Simulations and Experiments in Protein Folding
2014
The interplay between simulations and experiments of protein folding has largely contributed to the elucidation of many important aspects of the phenomenon. In this chapter, I briefly describe the experiments which provide information on the kinetics of the protein folding process, and help to characterize the folding transition state. Then, I show how to probe the kinetics of protein folding using molecular dynamics simulations, how to compare the simulations with the experiments and how to help and rationalize the latter, ultimately offering a molecular picture of the process. After the production of suitable molecular dynamics simulation data in the form of trajectories, the procedure in…
All-or-none proteinlike folding transition of a flexible homopolymer chain.
2009
Here we report a first-order all-or-none transition from an expanded coil to a compact crystallite for a flexible polymer chain. Wang-Landau sampling is used to construct the complete density of states for square-well chains up to length 256. Analysis within both the microcanonical and canonical ensembles shows a direct freezing transition for finite length chains with sufficiently short-range interactions. This type of transition is a distinctive feature of "one-step" protein folding and our findings demonstrate that a simple homopolymer model can exhibit protein-folding thermodynamics.
A photoswitchable helical peptide with light-controllable interface / transmembrane topology in lipidic membranes
2021
AbstractAccording to the three-step model, the spontaneous insertion and folding of helical transmembrane (TM) polypeptides into lipid bilayers is driven by three sequential equilibria: solution-to-membrane interface (MI) partition, unstructured-to-helical folding, and MI-to-TM helix insertion. However, understanding these three steps with molecular detail has been challenged by the lack of suitable experimental approaches to rapidly and reversibly perturb membrane-bound hydrophobic polypeptides out of equilibrium. Here, we report on a 24-residues-long hydrophobic α-helical polypeptide, covalently coupled to an azobenzene photoswitch (KCALP-azo), which displays a light-controllable TM/MI eq…
Kinetic Studies of the Assembly of Plant Light Harvesting Complex II
1998
Photosynthesis relies on the correct assembly of pigment binding proteins within the thylakoid membrane. Yet, very little is known about the folding of such membrane proteins. The biochemical difficulties connected with these highly hydrophobic proteins are reflected in the low number of crystal structures available for membrane proteins to date. One of the few available, however, is that of LCHII (1). In addition, LHCII is one of only a handful of membrane proteins that can be regenerated in vitro to a native-like conformation (2,3). These two features make it a good candidate for studying its folding and assembly kinetics. Here, a preliminary study on the assembly kinetics of LHCII as a f…