Search results for "folding"
showing 10 items of 330 documents
Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity
2012
Backbone modification is a common chemical tool to control the conformation of linear peptides and to explore potentially useful effects on their biochemical and biophysical properties. The thioamide, ψ[CS-NH], group is a nearly isosteric structural mimic of the amide (peptide) functionality. In this paper, we describe the solution synthesis, chemical characterization, preferred conformation, and membrane and biological activities of three, carefully selected, peptide analogues of the lipopeptaibiotic [Leu11-OMe] trichogin GA IV. In each analogue, a single thioamide replacement was incorporated. Sequence positions near the N-terminus, at the center, and near the C-terminus were investigated…
Methionine in a protein hydrophobic core drives tight interactions required for assembly of spider silk
2019
Web spiders connect silk proteins, so-called spidroins, into fibers of extraordinary toughness. The spidroin N-terminal domain (NTD) plays a pivotal role in this process: it polymerizes spidroins through a complex mechanism of dimerization. Here we analyze sequences of spidroin NTDs and find an unusually high content of the amino acid methionine. We simultaneously mutate all methionines present in the hydrophobic core of a spidroin NTD from a nursery web spider’s dragline silk to leucine. The mutated NTD is strongly stabilized and folds at the theoretical speed limit. The structure of the mutant is preserved, yet its ability to dimerize is substantially impaired. We find that side chains of…
Clusterization and Strong Coulpled-Channels Effects in Deuteron Interaction with 9Be Nuclei
2019
Angular distributions of protons, deuterons, tritons and alphaparticles emitted in the d + 9Be reaction at Elab=19.5 and 35.0 MeV have been measured. The elastic scattering channel is analysed in the framework of both the Optical Model and the Coupled-Channel approach. The interaction potential of the d + 9Be system is calculated in the framework of the Double-Folding model using the α + α + n three-body wave function of the 9Be nucleus. The (d, p) and (d, t) one-nucleon-transfer reactions are analysed within the coupledreaction-channel approach. The spectroscopic amplitudes for the different nuclear cluster configurations are calculated. Differential cross sections for the reaction channel…
The Modifying Mirror
2023
Abstract This chapter compares music listening with the infant’s experience of care. Several scholars have argued that music can be used for scaffolding one’s self-experience. Developmental psychologists, in turn, maintain a wide consensus over the claim that, in early interaction, the attuned caregiver supports and modifies the infant’s self-experience in various ways. The chapter brings these phenomena together, illustrating how the examination of the early self/other relation can teach us something important concerning the listener/music relation. The first section elaborates on the scaffolding function of music and clarifies two ambiguities haunting the debate. The second section reloca…
Educational dialogue in the classroom : scaffolding, knowledge building and associations with academic performance
2018
The present thesis focuses on patterns of educational dialogue, their quality with respect to forms of teacher scaffolding and shared knowledge building, and the association between the quality of educational dialogue and students’ academic performance. The specific questions of interest are as follows: (1) to examine how teachers scaffold students in learning situations through dialogic teaching, (2) to identify patterns of shared knowledge building in educational dialogues, and (3) to investigate how the quality of educational dialogue is associated with academic performance. The data were drawn from the audio- and video-recorded lessons of the First Steps longitudinal study, which were c…
Mechanics of invagination and folding: Hybridized instabilities when one soft tissue grows on another
2015
We address the folding induced by differential growth in soft layered solids via an elementary model that consists of a soft growing neo-Hookean elastic layer adhered to a deep elastic substrate. As the layer/substrate modulus ratio is varied from above unity towards zero we find a first transition from supercritical smooth folding followed by cusping of the valleys to direct subcritical cusped folding, then another to supercritical cusped folding. Beyond threshold the high amplitude fold spacing converges to about four layer thicknesses for many modulus ratios. In three dimensions the instability gives rise to a wide variety of morphologies, including almost degenerate zigzag and triple-ju…
Understanding membrane protein folding and interfaciality
2021
Despite the bast abundance of membrane proteins encoded in the human genome, the understanding of their biosynthesis and folding is far from the knowledge we have of soluble proteins. In the present thesis the main objective is to increase our knowledge on membrane protein biogenesis and folding, from the first steps of folding within the ribosome to the native structure acquisition in the membrane. Hydrophobicity, helicity and length of the polypeptide chain have been stablished as the major determinants for alpha-helical conformation adoption within the ribosome exit tunnel. Also, a 'biological' interfacial scale for the 20 naturally occurring amino acids were determined due to the develo…
Deterministic folding in stiff elastic membranes.
2008
Crumpled membranes have been found to be characterized by complex patterns of spatially seemingly random facets separated by narrow ridges of high elastic energy. We demonstrate by numerical simulations that compression of stiff elastic membranes with small randomness in their initial configurations leads to either random ridge configurations (high entropy) or nearly deterministic folds (low elastic energy). For folding with symmetric ridge configurations to appear in part of the crumpling processes, the crumpling rate must be slow enough. Folding stops when the thickness of the folded structure becomes important, and crumpling continues thereafter as a random process.
Viroporins, Examples of the Two-Stage Membrane Protein Folding Model
2015
Viroporins are small, α-helical, hydrophobic virus encoded proteins, engineered to form homo-oligomeric hydrophilic pores in the host membrane. Viroporins participate in multiple steps of the viral life cycle, from entry to budding. As any other membrane protein, viroporins have to find the way to bury their hydrophobic regions into the lipid bilayer. Once within the membrane, the hydrophobic helices of viroporins interact with each other to form higher ordered structures required to correctly perform their porating activities. This two-step process resembles the two-stage model proposed for membrane protein folding by Engelman and Poppot. In this review we use the membrane protein folding …
Dynamic Refolding of Ion-Pair Catalysts in Response to Different Anions.
2019
Four distinct folding patterns were identified in two foldamer-type urea-thiourea catalysts bearing a basic dimethylamino unit by a combination of X-ray crystallography, solution NMR studies, and computational studies (DFT). These patterns are characterized by different intramolecular hydrogen bonding schemes that arise largely from different thiourea conformers. The free base forms of the catalysts are characterized by folds where the intramolecular hydrogen bonds between the urea and the thiourea units remain intact. In contrast, the catalytically relevant salt forms of the catalyst, where the catalyst forms an ion pair with the substrate or substrate analogues, appear in two entirely dif…